Scotty.. This will be a simple fix, with a bit of luck.
Check the pushrods are correctly located in the ends of the rocker cups. Then reset the tappet clearances. Easy to back off the adjusters, get the pushrod on the back of the cam, then raise the rocker and makes sure the pushrod enters the cup. Mis- aligned is how they get bent.
It may be an ignition problem, try substituting the HT leads, lead for lead, not swapping them side to side. Nothing you have done to the head will affect the ignition timing.
Backfiring in the exhaust can also be a weak mixture, but more likely in both pipes. As you have had the top off, the pushrods are a good place to start.
Swarfy.