Firstly, let me say you're doing a nice job. I got this running on a NES emulator for the Playstation Portable, and it seems to run well.
Secondly, the music makes my ears bleed. The arrangements are lovely imitations of Final Fantasy tracks, but ARGGHHH! THE CHIRPING NOTES!!! THE PAIN!!! MIGRANES!!! I think nes chiptunes are a wee bit overrated. @_@
Non-stop random encounters aside, you've done a good job polishing up the combat and environments. I played an original rom alongside yours, and the difference was staggering.