[Laird Scooby]

Just a suggestion here from an experience i had with mine recently. Although the cam timing is correct, is the cam belt tension correct? If it's not quite tight enough it will allow the timing to "wander" causing flat spots, might be worth checking before delving too deeply into electrical gremlins. Not sure on yours if the ignition timing is adjustable, could be they set the timing without getting it properly warm in which case the cold start advance (if it has it, my 740 does) might still be operating resulting in apparently correctly set ignition timing but once warm it is several degrees retarded.