After searching around a bit I found out you can indeed back-up substance but you either have to take out skateboarding or specials, snake tales and vr missions. Still haven't found a guide on how you do this exactly but if anyone can find a guide please post it.
I found a guide on how to back up substance on 2 dvd5's. It doesn't seem too hard but I'll find out for myself once I can get a hold of $ony's cd/dvd generator. Here's the guide. Introduction: This tutorial will allow you to successfully back-up a legal DVD9 disc of Metal Gear Solid: Substance that you own onto (2) DVDR discs using a DVD burner. Please NOTE in advance that while both discs work and the game itself is fully playable using a mod-chip or the Swap Magic v2.0 discs, due to the way the Swap Magic handles games with Multiple ELF files on a v7 PS2 console it will cause the SKATEBOARDING side-game to RSOD (Red Screen Of Death) if you select it. We at Team PS2Ownz look forward to the upcoming ZoneLoader (www.zoneloader.com) alternative PS2 Boot Disc to FIX this issue, so be sure to stay tuned to www.ps2ownz.com for the latest news on it! If you have a v1-v6 PS2 console and are using the Swap Magic v2.0 disc, then simply swap using the CDLoader Disc available for download on several Web sites and the SKATEBOARDING side-game will work fine! Also, if you have a solder-in Magic/Messiah/DMS/NEO chip, you should be able to play the SKATEBOARDING side-game with no problems of course! Wink Extracting your DVD9 disc image: There are many pieces of software one can use to extract their DVD9 disc image of Metal Gear Solid: Substance to their hard disk drive, but the one I am using for this tutorial is DVD Decrypter (www.dvddecrypter.com). Once the software is installed and your original DVD9 game disc is in your DVD reader drive, simply open DVD Decrypter and set the MODE to ISO->READ followed by clicking the Decrypt button at the bottom of the GUI window. Make sure you have enough space on your destination drive for the image to be created, and watch it create your ISO image from your original Metal Gear Solid: Substance disc! Splitting/Extracting your DVD9 ISO image layers: Once your DVD9 ISO is created, you must split the two layers (layer0 and layer1). For this task, I recommend using ISOEdit v1.0 by Sonix. This freeware utility can be found on many Web sites including www.ps2ownz.com and www.alucard.cc so if you can’t find it just ask on the DVD9 ripping forums. To split and extract both layers from your DVD9 ISO of Metal Gear Solid: Substance simply open up ISOEdit and click on the folder icon to Open ISO File by navigating in Windows where your ISO image was created and selecting it. After you open it, you will see directories (folders) in the left window and files in the right window from the first layer (layer0). Highlight each file, click the Extract File(s) button, and extract each to a desired location on your hard disk drive... but be sure to keep the correct files in their corresponding folder by labeling your new folders EXACTLY as the directories you are extracting the files from. Once you do this to ALL of the folders in the left window of ISOEdit, then it is time to click the Switch Layers button to perform the same process to the second layer (layer1) files. It will take several minutes to do this task! Once ALL files from both layers are extracted: The next step in ripping Metal Gear Solid: Substance into (2) DVDR discs is to get rid of the DVD9/DVD checks. In this case, they are located in 3 FILES from ALL of those you just extracted. Here are the three that MUST be altered: SLUS_205.54 \MODULES\IOPRP255.IMG \SKATE\IOPRP255.IMG The second and third are inside the corresponding directory listed, so be sure to NOTE that as the identical IMG file appears twice in the ISO. To remove the DVD9 checks from the SLUS_205.54, simply open up WinHex (www.winhex.com), select FILE->OPEN from the top menu, and then navigate to the SLUS_205.54 file that you extracted from the DVD9 ISO and click OPEN. You will now see a bunch of raw code from the file on your screen in WinHex, so next select Position->Go To Offset and make sure that the Bytes are set to hexadec. If not, go to Options->General and select (check) Hexadecimal offsets followed by clicking OK. In the Go To Offset GUI window, enter in the following offsets under New position (one at a time) ensuring the relative to... radio button is selected next to beginning of file. Here are the offsets and bytes to change for the SLUS_205.54: 6F4: 01 change to 00 80B91: 01 change to 00 80B9D: 01 change to 00 80BA9: 01 change to 00 80BB5: 01 change to 00 80BC1: 01 change to 00 80BCD: 01 change to 00 Be sure when making these changes to OVERWRITE them- do not INSERT them nor press BACKSPACE... use the directional arrow keys to navigate around if you must! Now, SAVE your “modified” SLUS_205.54 file and open the \MODULES\IOPRP255.IMG file in WinHex. You will now see a bunch of raw code from the file on your screen in WinHex, so next select Position->Go To Offset and make sure that the Bytes are set to hexadec. If not, go to Options->General and select (check) Hexadecimal offsets followed by clicking OK. In the Go To Offset GUI window, enter in the following offsets under New position (one at a time) ensuring the relative to... radio button is selected next to beginning of file. Here are the offsets and bytes to change for the \MODULES\IOPRP255.IMG file: 1F024: 00 change to 01 1F026: 40 change to 03 1F027: AE change to 24 1F046: 00 change to 43 1F047: 00 change to AE 1F060: 2B change to 01 1F061: 10 change to 00 1F063: 00 change to 24 1F190: 2B change to 01 1F191: 18 change to 00 1F193: 00 change to 24 22C4E: C0 change to 00 Be sure when making these changes to OVERWRITE them- do not INSERT them nor press BACKSPACE... use the directional arrow keys to navigate around if you must! Now, SAVE your “modified” \MODULES\IOPRP255.IMG file and open the \SKATE\IOPRP255.IMG file in WinHex. You will now see a bunch of raw code from the file on your screen in WinHex, so next select Position->Go To Offset and make sure that the Bytes are set to hexadec. If not, go to Options->General and select (check) Hexadecimal offsets followed by clicking OK. In the Go To Offset GUI window, enter in the following offsets under New position (one at a time) ensuring the relative to... radio button is selected next to beginning of file. Here are the offsets and bytes to change for the \SKATE\IOPRP255.IMG file: 1F024: 00 change to 01 1F026: 40 change to 03 1F027: AE change to 24 1F046: 00 change to 43 1F047: 00 change to AE 1F060: 2B change to 01 1F061: 10 change to 00 1F063: 00 change to 24 1F190: 2B change to 01 1F191: 18 change to 00 1F193: 00 change to 24 22C4E: C0 change to 00 Be sure when making these changes to OVERWRITE them- do not INSERT them nor press BACKSPACE... use the directional arrow keys to navigate around if you must! Now, SAVE your “modified” \SKATE\IOPRP255.IMG file. CONGRATULATIONS- YOU HAVE REMOVED ALL OF THE DVD9 CHECKS AND THESE “MODIFIED” FILES CAN NOW BE USED FOR DISC1 AND DISC2 !!! Smile Creating Disc #1 required DUMMY files: Before building Disc #1, a few DUMMY (zero-data) files are required to be added/replaced in your extracted files and directories. First off, combine both of your MGS2 directories from both layers if you haven’t already so that ALL the files are in a single folder named MGS2. Now, remove the DEMO2.DAT, STAGE2.DAT, and the VOX2.DAT files from this directory and place them someone else on your PC or delete them as they aren’t needed for Disc #1. Use one of the MANY dummy file programs on the net (ISOEdit v1.0 can also be used on them if you load your original DVD9 ISO image in it) to create zero-data blank DUMMY files named the following... and replace them in your \MGS2 folder: DEMO2.DAT STAGE2.DAT VOX2.DAT OK... you are ready for building your Disc #1 DVDR ISO image! Building Metal Gear Solid: Substance Disc #1 of 2: The freeware utility CDGenPS2 can be used to build your Disc 1 ISO, but it requires a Tree File from ISOBuster (posted later in this tutorial) so we will build our disc without one using CD/DVD-ROM Generator v1.50. However, this software is COPYRIGHTED so please do NOT ask where to get it on our Web site or Forums... or you will get BANNED unfortunately! Once you open CD/DVD-ROM Generator v1.50, click OK to Create new project, and select DVD-ROM Master Disc and click OK again. Next, click on the Volume button in the top menu and for Disc Name enter SLUS 20554 in the two boxes to the right. Be sure the License Area is set to America, and then click on the Directory button. Now, in Windows find the place where all of your Metal Gear Solid: Substance DVD9 ISO extracted (and modified) files in their corresponding directories are located, and highlight them all dragging EVERYTHING into the right-side Directory window in CD/DVD-ROM Generator v1.50. Click on Options->Preference and be sure the Default Area is set to America, and that Disc ID is set to Enable and press OK. Finally, click on the Rec... button in the top menu of CD/DVD-ROM Generator v1.50 and be sure you have enough free space on your hard disk drive for the software to compile your Disc #1 ISO. If you do, enter an IML File name when prompted to (it can be anything you want it to be) and click SAVE. You will now see a GUI pop up, select your DVD burner if it isn’t selected already, select your burning speed, and click the Rec button followed by clicking OK to the prompt proceeding it. Again, enter an LST File name when prompted to (it can be anything you want it to be) and if you plan to burn Disc #1 immediately following the image compilation then insert a BLANK DVDR into your DVD burner and click SAVE. If you don’t have a disc in your burner, then the image will build, but not burn after it is finished building automatically. Sit back and wait... visit www.ps2cover.com if you’d like, and about 45 minutes later you’ll have a Disc 1 DVDR back-up of Metal Gear Solid: Substance! Creating Disc #2 required DUMMY files: Before building Disc #2, a few DUMMY (zero-data) files are required to be added/replaced in your extracted files and directories. First off, combine both of your MGS2 directories from both layers if you haven’t already so that ALL the files are in a single folder named MGS2. Now, remove the DEMO.DAT, MOVIE.DAT, and the VOX.DAT files from this directory and place them someone else on your PC or delete them as they aren’t needed for Disc #2. Use one of the MANY dummy file programs on the net (ISOEdit v1.0 can also be used on them if you load your original DVD9 ISO image in it) to create zero-data blank DUMMY files named the following... and replace them in your \MGS2 folder: DEMO.DAT MOVIE.DAT VOX.DAT Next, for Disc #2 you will need to do something a bit different... you will need to take your STAGE2.DAT file and rename it to STAGE.DAT, and then DUMMY your STAGE2.DAT file... and replace it also in your \MGS2 folder: STAGE2.DAT *** TO REPEAT: FOR DISC2, YOU WILL NEED TO RENAME STAGE2.DAT TO STAGE.DAT SO THAT STAGE.DAT WILL BE 1.22 GB (1,313,384,448 bytes) IN SIZE TOTAL... AND THEN DUMMY YOUR STAGE2.DAT FILE. *** OK... you are ready for building your Disc #2 DVDR ISO image using the .DAT files you just modified as well as the SLUS_205.54 and IOPRP255.IMG file which you modified when creating Disc #1 in this tutorial! Building Metal Gear Solid: Substance Disc #2 of 2: Once you open CD/DVD-ROM Generator v1.50, click OK to Create new project, and select DVD-ROM Master Disc and click OK again. Next, click on the Volume button in the top menu and for Disc Name enter SLUS 20554 in the two boxes to the right. Be sure the License Area is set to America, and then click on the Directory button. Now, in Windows find the place where all of your Metal Gear Solid: Substance DVD9 ISO extracted (and modified) files in their corresponding directories are located, and highlight them all dragging EVERYTHING into the right-side Directory window in CD/DVD-ROM Generator v1.50. Click on Options->Preference and be sure the Default Area is set to America, and that Disc ID is set to Enable and press OK. Finally, click on the Rec... button in the top menu of CD/DVD-ROM Generator v1.50 and be sure you have enough free space on your hard disk drive for the software to compile your Disc #2 ISO. If you do, enter an IML File name when prompted to (it can be anything you want it to be) and click SAVE. You will now see a GUI pop up, select your DVD burner if it isn’t selected already, select your burning speed, and click the Rec button followed by clicking OK to the prompt proceeding it. Again, enter an LST File name when prompted to (it can be anything you want it to be) and if you plan to burn Disc #2 immediately following the image compilation then insert a BLANK DVDR into your DVD burner and click SAVE. If you don’t have a disc in your burner, then the image will build, but not burn after it is finished building automatically. Sit back and wait... visit www.ps2cover.com if you’d like, and about 45 minutes later you’ll have a Disc 2 DVDR back-up of Metal Gear Solid: Substance! Final Notes: In case you haven’t figured it out by now, Disc #1 of this (2) DVDR rip of Metal Gear Solid: Substance contains everything except MISSIONS and SNAKE TALES from the main menu of the game. If you want to play either of those selections without the game crashing, you will have to use Disc #2 of course to play them... however, on Disc #2 much of the other selections may crash which is why this is a (2) DVDR rip. Disc 1 FileList.txt file for our fellow rippers: 0000322 , I:\SYSTEM.CNF 0000323 , I:\MODULES\IOPRP250.IMG 0000453 , I:\MODULES\IOPRP252.IMG 0000583 , I:\MODULES\IOPRP253.IMG 0000714 , I:\MODULES\IOPRP254.IMG 0000844 , I:\MODULES\IOPRP255.IMG 0000974 , I:\MODULES\MODULE.IPK 0001156 , I:\MODULES\PLD.IRX 0001157 , I:\SKATE\FBD\SKATE2.FBD 0010285 , I:\SKATE\IOPRP255.IMG 0010415 , I:\SKATE\MODULES\LIBSD.IRX 0010429 , I:\SKATE\MODULES\MCMAN.IRX 0010476 , I:\SKATE\MODULES\MCSERV.IRX 0010480 , I:\SKATE\MODULES\MCXMAN.IRX 0010483 , I:\SKATE\MODULES\MCXSERV.IRX 0010486 , I:\SKATE\MODULES\MTAPMAN.IRX 0010492 , I:\SKATE\MODULES\PADMAN.IRX 0010514 , I:\SKATE\MODULES\SDRDRV.IRX 0010518 , I:\SKATE\MODULES\SIO2MAN.IRX 0010522 , I:\SKATE\SKATE2.ELF 0012032 , I:\SKATE\SOUND\BGMDATA.BIN 0012033 , I:\SKATE\SOUND\MAIN.IRX 0012139 , I:\SKATE\SOUND\SEDATA.BIN 0012178 , I:\SKATE\SOUND\STRBGM.VAS 0016805 , I:\SKATE\SOUND\VOICE0.BIN 0024845 , I:\SKATE\SOUND\VOICE1.BIN 0041270 , I:\SKATE\SOUND\WAVEDATA.BIN 0046943 , I:\SLUS_205.54 0047360 , I:\MGS2\CODEC.DAT 0074883 , I:\MGS2\DEMO.DAT 0801430 , I:\MGS2\DEMO2.DAT 0801431 , I:\MGS2\FACE.DAT 0816621 , I:\MGS2\MOVIE.DAT 1075370 , I:\MGS2\MOVIEVR.DAT 1293979 , I:\MGS2\STAGE.DAT 1628644 , I:\MGS2\STAGE2.DAT 1628645 , I:\MGS2\VOX.DAT 2240315 , I:\MGS2\VOX2.DAT Disc 2 FileList.txt file for our fellow rippers: 0000322 , I:\SYSTEM.CNF 0000323 , I:\MODULES\IOPRP250.IMG 0000453 , I:\MODULES\IOPRP252.IMG 0000583 , I:\MODULES\IOPRP253.IMG 0000714 , I:\MODULES\IOPRP254.IMG 0000844 , I:\MODULES\IOPRP255.IMG 0000974 , I:\MODULES\MODULE.IPK 0001156 , I:\MODULES\PLD.IRX 0001157 , I:\SKATE\FBD\SKATE2.FBD 0010285 , I:\SKATE\IOPRP255.IMG 0010415 , I:\SKATE\MODULES\LIBSD.IRX 0010429 , I:\SKATE\MODULES\MCMAN.IRX 0010476 , I:\SKATE\MODULES\MCSERV.IRX 0010480 , I:\SKATE\MODULES\MCXMAN.IRX 0010483 , I:\SKATE\MODULES\MCXSERV.IRX 0010486 , I:\SKATE\MODULES\MTAPMAN.IRX 0010492 , I:\SKATE\MODULES\PADMAN.IRX 0010514 , I:\SKATE\MODULES\SDRDRV.IRX 0010518 , I:\SKATE\MODULES\SIO2MAN.IRX 0010522 , I:\SKATE\SKATE2.ELF 0012032 , I:\SKATE\SOUND\BGMDATA.BIN 0012033 , I:\SKATE\SOUND\MAIN.IRX 0012139 , I:\SKATE\SOUND\SEDATA.BIN 0012178 , I:\SKATE\SOUND\STRBGM.VAS 0016805 , I:\SKATE\SOUND\VOICE0.BIN 0024845 , I:\SKATE\SOUND\VOICE1.BIN 0041270 , I:\SKATE\SOUND\WAVEDATA.BIN 0046943 , I:\SLUS_205.54 0047360 , I:\MGS2\CODEC.DAT 0074883 , I:\MGS2\DEMO.DAT 0074884 , I:\MGS2\DEMO2.DAT 0228318 , I:\MGS2\FACE.DAT 0243508 , I:\MGS2\MOVIE.DAT 0243509 , I:\MGS2\MOVIEVR.DAT 0462118 , I:\MGS2\STAGE.DAT 1103419 , I:\MGS2\STAGE2.DAT 1103420 , I:\MGS2\VOX.DAT 1103421 , I:\MGS2\VOX2.DAT