P.S. Have you figured out how many hours you've got into it?
Hours? Do not mention hours to my wife... I have more hours on the manual, than on the build, and almost as many hours trying to
find parts as on the build. Setting motor, transmission, & transfer case was the easy part. I scored on another engine w/small knock in bottom that had emissions electronics on it to replace my broken ones. It was a BIG score, because my motor came out of a rear-ended vehicle (that had been sandwiched) and cooling manifold under intake was broken, the front cover on mine cracked when tightening after replacing water pump, catalytic converters were smaller, ETC.
Making wiring and connections really ate up time, and presented biggest gremlins.
I have came to the conclusion that the 1601 DTC communications failure from not having a BCM is putting the ECM in FAIL SAFE MODE, causing the TCM to do same thing resulting in only having 3rd and 4th gears and no lockup. As I said, it is not a rocket on take-off, but no slower than the old tracker was, so I can imagine what yours must be like with a first and second range working.
Now to find a BCM, with connectors/plugs. I ended up making one of the connectors for TCM, and the BCM has more connectors.
I am using Tracker radiator with electric fan, engine temp likes to run at 205 (when idling), but book says thermostat is full open then, so not worrying yet. What is your temps running at?