I'd like to confirm that 1.002 works properly on Mednafen. The issue after finishing Level 1 is no longer around, and currently I'm at Level 3, which keeps kicking my ass even from the beginning.
I like how your partner now goes around helping you, although personally I feel like you could make the AI a bit more intuitive, instead of always following you from behind.
Also, for another suggestion, maybe make the controls readjustable, as they can still be confusing at times.