Regarding the split screen effect: I noticed an identical effect when messing around with bad scroll values in the Mega Man 2 editor. The pause menu would fix it and everything.
I tried to make a fixed graphics script for Rockman 1, but FCEUX's API is too limited. I wanted to take the minimap script (which uses hardcoded images) and scale it up to a fullmap (I've done that sort of thing before), but you can't really draw between the BG and object layer. If you disable the BG layer, those pixels show up as black. You could theoretically draw your image pixel by pixel, only overwriting black pixels, but then it would screw with sprite outlines and transparency.
There's a Super Metroid graphics fix script that actually simulates the game's drawing routine in Lua. It's pretty wild. FCEUX does not provide direct access to PPU RAM, so you'd have to write graphics through the port ($2007) if you wanted to go that route. That honestly might be the best way to do it, but it sounds really annoying to make!
Actually, now that I think about it, I bet you could disable
all graphics, do the minimap/fullmap thing, then just simulate the sprite drawing routine.
Also, I can't stop by without reposting my
coffeepasta! Did you guys have fun tracing those obscure race conditions from the 80's?