This is almost a whole new engine in thing? The list of what has not been changed has now got to be smaller??
With the vast amount of things that has been changed and checked I get the feeling this may be an electrical problem, probably a simple one at that. It seems that some connection somewhere is contracting away from making contact when cold.
Think I would try and unplug and re-plug every electrical connector and connection in and around the engine bay and make sure you give all other wires a wiggle too. This would include wires to all the sensors (unlug and re-plug) or wiggle as necessary, wiggle and check wires to maf, fuse boxes, and especially spark plugs, coils and the fuel pump.
Clutching at straws I know but it really does seem that almost everything else has either been done or changed.
Hope you get it sorted, it's been a right PITA.
