when you say you swapped the powerheads over what do you mean exactly:
1. Undressed the old, failed powerhead and transferred everything onto the "new" powerhead.
2. Lifted the "new" powerhead lock, stock and barrel and swapped over.
If it's option two then you've swapped ignition components from the "new" engine?
Have you checked the temp that the "new" head is running at?
Did you decoke the "new" head or just transfer it straight across?
Did you compare engine numbers and the year of manufacture of the powerheads.
Sorry for all the questions but the more info we have the better the chances that we might collectively spot the problem.