It is possible that someone in the past has the distributor installed one tooth off and instead of finding that they have been modifying the distributor caps. I find it unlikely that very many replacement caps would have the aligning tabs wrong. It sounds like you're on the right track to go back to basics, confirm TDC, confirm the cam position that both intake & exhaust valves are 100% closed THEN make sure the distributor points at #1 on the cap. The only things left are compression, spark and fuel for a running engine.
