I believe I may have sorted this out. I found a bunch of information available at ApplianceJunk.com that gave me pin outs, thermistor resistances + expected voltages, and the service manual for a later model of this unit.

Using that info I went through the thermistor voltages on with the old mainboard installed and they were both oscillating and going out of range.

During that process I noticed that the wiring on J1 pin 2 looked very similar to a step in in the WR55X10942 installation instructions that I _didn't do_. I skipped it because I though it said it was for a Bottom Freezer. So I went back and re-read the instructions and realized that the Note: is an OR condition bottom freezer or this list of prefixes on the serial numbers. My model serial numer prefix (LF2) was on the list.

So I cut the thermistor jumper wire connecting pin 1 and pin 2 of J1 and re-installed the new mainboard. Re-checked the thermistor voltages and they were not solid. The evap and freezer thermistors were a bit high 3.7V. The service manual says the max should be 3.5V. Checking the resistance of the sensors with the connector pulled shows them to be in the expected range. So for not I'm not going to worry about that.

After a brief boot up pause the unit turned on the compressor and evap fan as expected. Then later on when I checked the freezer it appears to have gone into low-speed evap fan mode. It was running but much quieter and after I had the door open for a bit it kicked up into high speed.

Previously none of that happened. I'm going to monitor the temperature for a few weeks and watch for the slow creep up that indicates its freezing up again but hopefully things are back to working.