Aaaaand now the game saves automatically while playing. Tested and working on a real NES using a powerpak (thanks protomank!). It works on nintendulator, fceux and nestopia. Resetting the game freezes on virtuanes (need to hardware reset), otherwise it's also playable there. It also works on wii's homebrew fceultra.
What happened is that I readapted infidelity's mmc3 patch and now the rom is mmc3 again. One thing that wasn't clear while trying to change mappers is that the header must also be editted. I used NESHEAD tool for this.
The thing about this is that someone can reset after finishing and can continue on the same save to try and go for the perfect ending (or erase and start over).
I have also fixed Harry's shooting animation. Turns out it was not a bug, it was an intentional animation. Now that I know asm a bit better I could see clearly the intent in the code.
shoot frame with gun > jump frame > shoot frame with gun
I changed to:
shoot frame without gun, eyes closed > shoot frame with gun, eyes opened > shoot frame without gun, eyes closed
The pause was also fixed, now it isn't too sensitive.