Actually I don't believe that transmission codes will actually trip the CEL
They WILL set codes in the computers memory, as "hard faults", but the CEL won't light.
I would STILL strongly recommend installing a manual trans computer, because idle strategy is different.
The primary difference is on a manual trans truck with the throttle closed and engine rpm above 1700rpm the computer turns the injectors OFF, so any time you are coasting you aren't burning a drop of fuel.
The "wiring harness" is NOT DIFFERENT between a manual trans an an auto.
there is a SEPERATE harness that plugs into the "main harness" that IS different.
This is the same harness that connects to the oil pressure sender, oil level sensor and the 4.0's cannister purge solenoid
If you already have an '89-92 2.9 you can use your exsisting "Transmission"
harness and just ADD the two wires for the 4.0's cannister purge solenoid to
the exsisting connector.
MOST of the many, many wires are self contained in the harness for the 4.0 and ou need do nothing with them, though in the name of tidyness I'd recommend remiving them...
Like On my truck I used a '93 explorer harness and kept the big underhood fuse box.
I ended up using the two relays that were there for the ABS system to switch
my Fog and Driving lights

which was definatly neater than having a pair of relays screwed to the inner fender)
AD