You have to have pretty high compression with the .050" and flat top pistons. That cylinder could just be running lean. Its unlikely due to the two valves in one port head configuration. 1 and 2 would both be lean if that was the case. The water could be doing it, its been the constant thru this whole thing. All though, won't a cold cylinder run rich?? Is it the same camshaft? could it be ground wrong and be doing something funny to that cylinder?
That would be my next check, degree it and the one next to it.

Keep us posted, Joe H.