The transmission shop just called. I haven't driven the car yet, but he said it shifts smooth now.

I told him when I left the car that maybe there's no "vacuum leak", but it's possible there's a "partial vacuum leak" somewhere that would cause this. I previously replaced as many rubber hoses as I could see, but it's possible there's something under the car that I can't see.

They found one of the vacuum hoses not plugged in 100% of the way that was causing the problem.