One other potential thing an emulator could be doing is how it handles PRG-ROM bank switching.
As I recall, when PRG ROM is switched, it should be ANDed with maximum ROM bank.
I can't remember if the original game was dependent on it, but as an example:
if a game is 16 banks (last ROM bank is numbered 0F), then the emulator should be modify the swapped PRG bank value by AND #$0F.
With 32 banks, it would be AND #$1F.
So a write of bank value #$F8 would become bank 8 on a 16-bank game and bank 0x18 on a 32-bank game.
The one other reported issue I had with the translation I think was an original game bug: in the Tactical-RPG sections, play in Manual battle mode. Using Auto battle mode seems to cause the game to incorrectly determine your spawn location after returning to the normal map. (though I only checked it on a Japanese ROM through a save provided by the person who reported it, so I can't say for certain if it is ENTIRELY the original game's problem)