With the TCU unplugged the trans only uses third gear.
You said the tranny worked before pulling the engine, but now only has 1st and 3rd. According to the FSM, that indicates a problem with wiring to the transmission 2-4 brake duty solenoid, 2-4 brake timing solenoid or 2-4 brake dropping resistor.
Note the guide tabs on the top of connector B54 at the bottom of the image. (different than B55). The pic shows the connector side of the plug, not the wire side.
Key off. Unplug B54 from the TCU and check OHMS to a good ground on Pins 5, 8 and 17.
Pin 5 (Light green Red stripe wire) 10-16 OHMS.
Pin 8 (Orange wire) 2-4.5 OHMS.
Pin 17 (Yellow Blue stripe wire) 9-15 OHMS.
If any of those readings goes high (open circuit), then check the wires on connector B11 located on top where the trans mounts to the engine. Maybe a pin pushed out of the connector or bent over. Note in the wiring diagram that the wire colors change when they go through B11.
You can also check voltages of Pins 8, 17 and 5 of B11.
Warm up the engine and then turn it off, then turn the key to ON (no start) and check voltage on the following pins of the B11 TCU connector.
B54 Pin 8 Throttle fully closed 1.5 — 4.0 v. Throttle fully open. Less than 0.5 v
B54 Pin 17 Throttle fully closed. More than 8.5 v. Throttle fully open. Less than 0.5 v
B54 Pin 5 1st gear Less than 1 v. 3rd gear More than 9 v.