I managed to fix the issue. It looks like for some reason the MD5 hash still needed to be manually edited with saves from that specific Vita. I tried it with my other Vita and it ended up working fine. Did nothing differently between the two, so I have no clue why it wasn't working properly.

I've noticed while it converts the saves, upon loading them into the PC version, the game crashes. It appears to be an issue with the converted system.bin and system.binslot files. I'm going to do a little more testing to see if I can possibly find a workaround in the meantime. EDIT: Appears to just...