My guess would be the solder connections on U1 are touching somewhere. I had the same problem myself with one PCB I assembled and a couple of others have had that problem as well. I removed all the solder from U1 with some solder wick and started over with much better results the second time, as did the others I know of that were having the same problem.
As for the power and calibration, I also used Stan's method detailed in his video posted in the thread. I use alligator clips to connect the tester to track power (with nothing on the track) and did the calibration the same way, as memory serves. I use PH-180s for track power so no current limiting here and they go through my TIU to get to the track. As I recall from following along in the design process here, GRJ's final design drawings were meant to use track power to drive the TIU Tester so no external power source was needed.
For the definitive answers on calibration I would wait for GRJ or Stan's comments just to be sure (and safe). I am by no means even anywhere close to being as knowledgeable as either those guys, I'm still just a greenhorn.