UPDATE: So we put the old three speed trans back in the car -- it still drove the same. Hooked up a dwell meter and found the dwell was w-a-a-y-y off. Opened the distributor and found tiny brass filings in the cap and base. Looked like the rotor had been shearing away at the contacts in the cap. Thinking this is causing the engine to misfire, especially under load. New cap and rotor, or new distributor??
(Thanks for the tip, 1951plymouth -- hoping my R10 is not the problem after all)!