[78T/A462]

I just installed a rebuilt 400 in my dads trans am. I ran it for 20 minutes and had the rpms bewteen 1500-2200 to break the cam in for those 20minutes. At that time it was missing and had exhaust leaks coming from the heat crossover bewteen the heads and the intake. After the cam break in I changed the oil, filter and plugs and attempted to find the misfire. I set the motor at tdc, checked the rotor position. checked firing order and even re adjusted the valves to be on the safe side and the same misfire. Beings the heat risers weren't filled with aluminum I cut a very thin piece of sheetmetal and placed some gasket sealer on it, slid it right where the heat riser is on the head and it stopped the exh leak. Does anyone have any suggestions of what the misfire could be? Flat cam? Could I have burnt a valve with the exh leak during the cam break in?? Been on it for a week and im pretty frustrated already...Thanks for the help.