Try the other x68k emulator called XM6 - its should run what win68k wont.
I have also been wondering just how to play those 'famicom' ports (particularly Galaga). On my real x68k i have been able to play temporarily with the joystick but its flaky. so consider this a bump. i did read that certain games came with joypad/stick adapters, so you could use the consoles native pad with the x68k - maybe there was something similar used on these ports?? if there are any Japanese speakers reading this can you do a search and see if you can find anything out?