Since I wasn't getting anywhere, I figured the transmission might have simply been caked with dry and dirty fluid after sitting in the salvage yard's warehouse for a few years, so I added 9 oz of Auto-RX to the fluid and drove it for about 1500 miles (the manufacturer suggests 6 oz for 1000 miles but I figured they weren't allowing for caked fluid). Auto-RX is not a detergent or active cleaner, but is an ester treatment that soaks into the metal and pushes crap off the walls from behind. I figured that this stuff in conjunction with the detergents in the Dexron VI fluid ought to get the thing pretty well clean.
Yesterday I changed the fluid while swapping the tranny cooler, and the results are quite remarkable. The stuttering shift from 3/lockup to 4/lockup is almost completely gone and is still only perceptible because I am hyper sensitive to it. The hard shifts from drive to reverse and vice versa are gone as well. Overall shifts are as smooth as my Cadillac. Very nice results. I will probably do another fluid swap and also change the filter screen in another few thousand miles so that I can get whatever junk is left out of the system.
So I'm guessing that the valves were caked, and the thing just needed a good cleaning.