I don't have much input but am along for the ride. I had the same situation as you with my K1, I replaced everything on it with the ultimate coils and pamco, new plugs, new wiring harness, new carb internals, etc etc etc. I was fortunate enough to get it going great. I did have stock carb jetting, stock airbox, and stock pipes. thats about the only difference I can see. I wish you luck, it seems like you're going through the right processes to determine it. keep it up, hopefully it will be something silly.
how is your pamco wired into the harness? do you have the two green wires switched? usually it won't even start at all if they are reversed though...hmmm