#2: Solved. I found that the amp on from my M1-ATX wouldn’t trip a relay. So I changed the switching power for that relay with the output from my override switch. The makes the amps/LCD turn on when I want still but using the output from the M1 would have been cleaner.
#3: I haven’t worked on yet but the shuttle express is now hooked up so if it was hanging due to that, the problem will be gone.
#4: Solved. I ripped out my whole dash face again and ran a new wire from the LCD ground to the M1-ATX ground from the molex plug. Flicker/noise went away. I still have some rhythmic lines that one can see if you look very hard. I am almost positive this is related to refresh rate and not noise. It doesn’t look like noise at all. At some point I’ll mess with the refresh rate. I’ll see if the screen has other refresh rates at 720x480 mode.
The computer portion is completely working now. I just need to solve some audio issues before I’ll have sound though.