I've bought a japanese n64. When I opened it up to see the insides (to do the rgb mod), I found some kind of mod or custom repair. I have no idea what it is. Possibly it's only some repair/fix from nintendo, but who knows.
Please take a look at the attached images.
Edit: More info
MODEL: NUS-001 (JPN)
BOARD: NUS-CPU-04
S/N: NUJ13497556
Pin 28 of U10 is lifted and connected with the blue wire to bottom of the motherboard
:-\ looks to me like this was done to it. http://level42.ca/projects/ultra64/kmc64-howto/