I picked up a Nintendo board in a bulk purchase a few weeks ago. It's a DK Jr. hacked to a DK 3. It looks like a color prom is bad and the sounds are all DK Jr.
They have that version in MAME, although the colors look normal. Even has the KAZUTOME name instead of NINTENDO and DK Jr sounds. It also seems to run painfully slow at times, even though it's running 100%. Does that seem to happen on your PCB?
I dunno, unless money or storage is an issue, I'd keep it the way it is, even if it is a bootleg...of course, I kinda like bootlegs, as you can tell, given my username here