The issue with Chocobo Forest controls was caused by the mod after all, sorry for the inconvenience. I managed to fix it as well as a few other things I noticed through Tingcos' stream:
- Trauma boss now properly enters rage mode after both Dromas have been killed.
- Standard battle theme reverts back to normal after doing the secret boss in Ultimecia Castle (fixed in 2013 version as well).
- Cleaned up some dialogue and Rinoa's positioning on the White SeeD Ship.
Also removed the possibility of back attack for the 3 Grats encounter in BG-Training Center. Thanks to JLOUTLAW for pointing it out.
@levantine: Alright, so I'll leave the prison boss fight as it is for now. I was worried about this battle the most, as the pressure increases significantly with another Elite Soldier present. But knowing that you managed to defeat them after some tries is kind of relieving. Whenever you think a certain boss is too easy or too hard, let me know.
@Dealer1993: If you're only missing the default spells the characters start with, and everything else works as intended, then it appears to me that you didn't start a new game after installing the files using zzzdearchive, as levantine said. If you don't, you'd also miss some GF Abilities already learned by default, increased GF compatibility values and Edea starting at level 40 instead of 26, but if you are already past Elvoret, it's probably not worth starting all over again.
Just to make sure, can you confirm that the kernel.bin file (inside main.fs) has been installed correctly? You could easily check by having a look at Break or Pain spells. If Diablos' Pain inflicts damage in addition to status effects, and Break does earth-elemental damage, then all is good.