When I first saw this, I didn't think it was really you, Nebuleon. I remember you looking at N64 on the Zero on your github, but never thought it would come this far. This is incredible!
Welcome back to the forums, and excellent progress on this so far!
As far as C buttons go, you could try combinations, like SELECT+A = Right C. The C buttons in many games are used for the camera, or to select an item (Ocarina of Time), so that's a possibility.
P.S. Tested games on the JIT build so far.
For Banjo Kazooie, the opening cutscene runs full speed except for very rare frameskips as the camera goes up the stairs into Grunty's Lair. Game itself runs at... mostly full speed. I'd have to say around 40, maybe even 50 FPS by the looks of it. Slight sound skipping. Haven't tried the interpreter build yet. Graphics look perfect, I haven't found any graphical issues other than the sky flashed green for a second in the opening cutscene.
Kirby 64 runs fullspeed, but I can't get past the tutorial video because of the lack of mapped C buttons and/or the analog stick. There's a lot of screwed up graphics though. The text is bundled up in the corner of the screen.
Super Mario 64 runs the same as Banjo Kazooie. Slight slow down, no graphical issues so far.
Bomberman Hero seems to be full speed, but the screen is black. No video.
Ocarina of Time is maybe 20 FPS at the moment. No graphical issues so far.