Ben, looking back through your worklog I noticed that you removed the filtering caps from the composite and audio lines on the motherboard. Have you wired those back in line? I find that 90% of the time wiring them back in line after I remove them will give a better picture and help reduce interference. I only had one time where I wired them back in that it made it worse.
Also, if you still have access to the motherboard to do it, sand all of the edges of the motherboard again to make sure that absolutely none of the inner layers are touching the outer ones. When I wired up the 2nd mobo for SS's XGC the first time I tested it I had terrible video and audio interference. I took the board and resanded the edges and all was well.
I noticed also that it looks like you have the Wiikey mounted right on top of the A/V chip. Try moving anything you have mounted near the A/V chip away from it as far as you can. Not likely this is the issue, but you never know. Interference can come from those little actel chips if they are close enough to other critical components.
hope that helps man, I wanna see this thing finished in all its glory.