I'm sorry xttx, I have not looked into it. I had stepped away from ROM hacking for a few months. It was my intent to redo this Remastered hack, because there are quite a few problems with it. A lot of my code is causing lagging problems, there is a major bug with the weapon-switching/select combo, that pushes the values onto the stack, and would eventually crash the game. And aside from the nestopia bug you pointed out, there a couple of other quirks that I'm not happy about. This hack was my first CHR-ROM conversion and SRAM hack, and my code is very messy, and all over the place. And there are things that now, I would have done differently, especially as I have a better understanding at 6502 ASM.
I'm sorry for the inconvenience, but have patience. I plan on re-doing this soon.