I just got back from driving it about 40 miles or so out in the county. The only gear that gave me any trouble was fourth. After driving it some more now, what it seems like to me is that the tranny is just really picky about what speed you put it in gear at. There would be times when I would try to downshift to fourth, and I could feel that it would not engage, so I would cost down until it would let me into third. Then back up into fourth, and then fifth. Shifting up through the gears was hardly a problem, as long as I let it run up to about 2500 RPM before shifting to the next gear, with the exception of fifth, which was never a problem to get into. Is this normal, or indicative of a problem? Maybe it's like I said, and I just need to relearn to drive with a five speed, and I'm being overly sensitive to it.
I could see maybe some kind of internal rust; The tranny was shipped mostly dry, and I'm pretty sure most of the remaining fluid came out in transit. It sat for a month or so before I did the swap.