1990 4.0l will have an A4LD 4-speed with electronic controlled Torque converter and 3rd/4th shift.
There will be 3 wires connected to a D-shaped connector on the side of the transmission.
1 wire will have 12volts with Key On
Other 2 go to the computer, one locks torque converter, the other shifts the OverDrive(OD), the 3rd/4th shift.
But that's all it controls
Transmission in Drive should shift on its own from 1st to 2nd and 2nd to 3rd, if that doesn't happen then you have internal problems.
Automatics work on pressure, and higher RPM = higher pressure, when pressure gets high in one gear valves open and it shifts to the next gear, no shift means either valves are stuck or gaskets are leaking(no pressure build up).
But trans needs to come out in any case.
If the replacement trans was a rebuilt then it will be under warranty, if it was a used transmission you bought someone else's problem.
Good read here on A4LD:
When having an A4LD rebuilt, there are a couple of things that you need to make sure of. First and foremost, do not let a shop do a soft parts fix only (clutches, servos, and bands). This will almost ensure that you will have another repair needed right after the 1-year warranty is out. Other things you want to have replaced are: forward one-way clutch (always), overdrive drum (stamped tin, replace if out of round or heat damaged), pump (Ford only, rebuilds are prone to failure), and the converter (get the better converter with the improved lock-up clutch and brazed fins).