Did not receive any replies to my question, but if you are interested here is the rest of the story:
Short answer when the engine was replaced, the knock sensor was not plugged back in;
Knock sensors rarely go bad, except that a bad knock sensor (or one not plugged in) screws up the timing information to the transmission for shifting. (My non technical understanding of the cause)
Toyota dealer identified the problem (used a bore scope to snake under the intake manifold, had a hunch since the engine was replaced and knock sensors don't normally go bad) and I took it back to my engine installer who said "oh poop" and corrected it in short order.