Download the following tools (as needed):
- pkg2zip
- _decrypt.exe and psvpfsparser-win64.exe
- Total Commander
- PSARC plugin for Total Commander
- wxMEdit
- quickbms to unpack APAC files
Run this command pkg2zip.exe so2.pkg to get STAR OCEAN Second Evolution [PCSG00714] [JPN].zip

Extract the zip file. The contents should look like this

 \---app
     \---PCSG00714
         |   eboot.bin
         |   so2psv.psarc
         |
         +---GXM
         |   \---save
         |           ClearIcon.png
         |           EmptyIcon.png
         |           SaveIcon.png
         |
         +---sce_module
         |       libc.suprx
         |       libfios2.suprx
         |       libult.suprx
         |
         +---sce_pfs
         |       files.db
         |       pflist
         |       unicv.db
         |
         \---sce_sys
             |   clearsign
             |   icon0.png
             |   keystone
             |   param.sfo
             |   pic0.png
             |
             +---about
             |       right.suprx
             |
             +---livearea
             |   \---contents
             |           bg.png
             |           button.png
             |           template.xml
             |
             +---package
             |       body.bin
             |       head.bin
             |       stat.bin
             |       tail.bin
             |       temp.bin
             |
             \---trophy
                 \---NPWR09638_00
                         TROPHY.TRP

Copy work.bin into PCSG00714\sce_sys\package and run this command to decrypt files: _decrypt.exe PCSG00714
Unpack PCSG00714_dec\so2psv.psarc with Total Commander and PSARC Plugin
Unpacking PCSG00714_dec\so2psv.psarc should get you a folder called GMX, see contents here: so2psv.psarc.txt
Use QuickBMS with star_ocean_kcpa.bms to extract APAC files. Sample command to extract a single file: quickbms.exe -d star_ocean_kcpa.bms 017_ArliaW_20_branch001.apac
A hex editor like wxMEdit can be used to look at the contents.

Repacking PSVita Files

Use Total Command and the PSARC plugin to pack the files back into a single PSARC file
Select the GMX folder with with the modded files on the right side of Total Commander (right-click to highlight red)
Click on the "Pack file" button on the tool bar. Uncheck "Also pack pathnames" so the GMX folder doesn't appear again.
Click OK to save the file as GMX.PSARC, you can rename it to so2psv.psarc later.
Notice the newly packed file is a different size from the original, even if you don't make any modifications.

Unpacking PSP Files

Get PSP_GAME\USRDIR\so2pack.bin
Use QuickBMS with so2pack.bms to extract game files. Sample command: quickbms.exe -d so2pack.bms so2pack.bin
After extraction, there should be ~25,830 files with extensions like DAT, IMG, GIM, NFC, SDB, SLZ, TXT, VAP, and XEJ. See contents here: so2pack.bin.txt
Use QuickBMS again to further extract SLZ files. Sample command: quickbms.exe -F "{}.slz" slz.bms so2pack.bin_extract slz
There are more SLZ files in here, so run the command again to extract the files further. Files include CGM, and FOG extensions.

Packing PSP Files

Make a copy of so2pack.bin just in case.
Use QuickBMS to repack files into the existing so2pack.bin. Sample command: quickbms.exe -r -w so2pack.bms so2pack.bin so2pack.bin_extract
To repack files, the modified files need to be less than or equal to the original file.

Hacker Notes

This section is for notes found around the web that may help with this project.

Hacker Note 1

Note for anyone trying to patch ENG text. Entire game is one psarc file. ~~It's easily extracted and reencrypted.~~ ~~Structure appears same as PSP ver~~, so, ~~I think it is possibly easy to patch official PSP ENG translation~~.

Resources

QuickBMS script to unpack so2pack.bin (PSP)