I'll opt in with a wild-a** guess....
Check the plugs. I'm thinkin' that the intake is sealing on one head, but not the other. The bank that isn't sealing would therefore be drawing in a leaner mixture and running hotter and possibly mis-firing. Here's a routine I use on every motor I build since I figured out how to do it.....
http://streetmachinesoftablerock.com...opic.php?t=350