The reason the 5mt ECU won't work is because it has different trigger info. The crank teeth on a 5mt BE is the same as a wrx actually, so if you want it to work with that ecu you will need to change the crankshaft sprocket and the camshaft sprocket I believe as well. Your car is a 6 tooth crank and 7 tooth cam, the 5mt is something like a 40 tooth crank and 2 tooth cam I believe.
What I did I think was just kept my TCU plugged in, one plug was plugged in and the other was not(don't recall which one). I constantly had a CEL though but I could drive the car fine.
What sucks is you already had the motor out to do the timing belt...but if I were to do it over I'd prob want to swap those parts and run a 5mt ecu.
Hope that helps some.