I decided to have a try with the amp powered from another source and disconnecting the controller after I got into a game, so the only connections to the mobo were the screen and everdrive. Still got noise but even more strangely the audio had another issue, the balance of dialogue and music was well out of whack. In menu for Mario the "It's me Mario" and "Press start to play" are barely audible though the music is still in stereo. I'm powering the amp from a usb on my pc reading the exact same voltage as I was getting of the N64, very strange indeed, the fault finding continues.
Edit: just tried the PAM amp from the BOM, same audio issue there too.
Still haven't been able to get this working how I would like, not only can I not fix it but I can't even seem to improve it I'm stumped. Looks like I need to go the digital audio route which hopefully sorts it. This leaves me with an issue though, the volume rocker for the audio amp I have was going to be a wheel, since I can't use this with the digital amp and I have a slot for the volume control in my case already I'm left with what to do with that slot without any modification to the case.
I think a volume rocker could work given the small space there is to work with, I've done a quick sketch to envision how things could work. I'll have to make the rocker in fusion360 and print it, the rest can be done with pvc sheet and rod.
I was also wondering if it's possible to get me screen running off 5v. I saw a post that the KYV-N2 V6 can be modded, is is possible for a V1?
For the rocker:
Why not extrude the pivot down from the middle of the rocker itself to reduce the number of parts, or you could actually do away with the concept of the rocker entirely as pressing down on a tight-fit button like that will apply force to the tact switches at either end without needing a rocker setup.