1997 Dodge Neon computer issue?

I have a 1997 Dodge neon DOHC 5-speed that needed a new computer/ecm/ecu/brain box (whatever you call it!). Since I had to match the year, engine, and tranny up it was difficult to find a used computer. After getting a few that weren't correct I finally found one and I had the dealership confirm it being correct. Now when I put in into the car it throws 2 codes. One being p0743 torque convertor (since the car is manual and the computer came out of a manual I don't understand where this code is coming from) and the other code being p1490, which is a low speed fan relay circuit. Interestingly enough, the fans will not kick on with this computer plugged in even when the car starts to overheat, but when I plugged in one of the wrong computers I have the fans work fine. MY QUESTION IS THIS: If I get the dealership to program into the computer the VIN and mileage (which is the only thing they can program into it) will it fix the problem with the fans and it throwing the torque convertor code, or is this computer junk? I don't want to spend $100 getting it programmed if the computer is fried. Please help!

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