1. What difficulty mod are you using?
I installed Scene Redux - Better Steal mod, I thought it would just allow me to steal things quicker/easier, didn't know it changes whatever is available to steal, is there a list of changes somewhere? And is changing what's available to steal the only thing it does? Also, I take it that I have to reinstall the whole thing to fix it?
2. Need to follow the story. Many things in the game are triggered by previous events and how they unfold. Porting around skips these events, and although trainers work for unmodded games, the same may not apply for modded games. There is no way I can pinpoint that kind of issue as Bootleg is only meant to play the game through from start to finish without a trainer. You can try downloading the Black Chocobo tool and checking the box to allow Mystery Ninja Fights in Forests, but I don't know if that will really work. It also may not prevent future issues you could run into. If Black Chocobo doesn't work, than you can either port back to leaving Midgar and try continuing regularly, or load the closest save before your port and continue regularly.
I tried with Black Chocobo, it would allow me to get to fight her, but as soon as I executed one action, the battle would freeze and I can't do anything else at that point. So I'm guessing I have to replay it.
3. Again, because of the porting I can't pinpoint this at all. Normal playthroughs with Bootleg installed will not run into this issue, so it's more than likely due to the trainer. I don't know if Black Chocobo can help any with this.
I'm using the trainer that came with the bootleg, by Kranmer I believe, does it still clash with the system?
4. If you look at your Bootleg log, it can show whether it installed or not. Posting here is fine, but make sure you surround it with the code tags or else it's going to be an insanely long post.
I'm not sure where to look for it, sorry, can you tell me?
thanks for all your help so far.