I appreciate this advice. It is spot on. I checked the connections to every part of the system that I could think of. Everything is solid. New distributor and coil, one new wire. If setting the sync signal doesn't clear it up, then I will pull the injectors and reverse flush them into a white rag, using a 12 volt DC power source, per your recommendation.

None of these issues appeared until shortly after this trans rebuild. I do not think that the trans itself has caused any of this, but perhaps something happened during the install that contributed. I am not a big believer in coincidence, but perhaps that's what I'm facing here.