antblyme,
Well, if the timing was spot on with the stock rotor before you removed it, then it's spot on now. If the carbs were working great and you didn't do anything rude to them, then they are OK now as well. That just leaves the PMA, and although I cannot imagine how the PMA could cause your problem, that's the only thing you changed, so run the PAMCO off of the battery, and just for good measure, disconnect the PMA to completely eliminate it as a cause.
If you ever want to give yourself a little more room to set the timing on the PAMCO (not now, but after you fix this problem) then loosen the nuts on both the PAMCO rotor and the slotted disk on the advance side and then hold the rotor tightly clockwise as you tighten the nuts. That will give you all of the free play available to set the timing.