94 Explorer problem

Hi, I am hoping someone can help me with a self created problem, I recently pulled my auto tranny out of my Explorer, and replaced it with a 5 spd.(had a 91 standard scrapped).. everything went great, BUT as soon as I test drove it, it started to work real bad....if I keep the pedal to the floor for a few seconds, it picks up a bit till I back off the gas, then it starts again. Hook up a Monitor 4000 Enhanced, checked codes, it said ECT , so, changed the sensor,same thing,then drove it with the 4000E hooked up, runs great...no prob.. unhook the tool... works bad....I don't know what else to try..any ideas??? I tried the computer from the 91, but it won't run on it.. Maybe have to change back to the auto again???? Thanks, Rodger