Great, I'll see if there's anything else that can be added, but I think we've got most of what we know so far. Thanks!
Here's some offsets that you can add.
Layout:
Description, Offset, Size of data
General Flags, 0x00023bbc, 512 bytes: These flags control events (unlocked NPC, blueprints, etc.)
Abilities Aquired Flags, 0x00023bdc, 63 bytes: If you set any of these flags, they will not show up in the crystal, but they will show up when setting your abilities. You can fix it by setting other flags within the save file.
Jobs Unlocked Flags, 0x00023dfb, 3 bytes: If you set any of these flags, you will not unlock anything that you would have if you did it legit. This can be fixed by playing the game or setting other flags within the save file.
***The flags are set by the bits, not the bytes.***