powertrain control module help (jeep tech)

OK I am still trying to track down this engine stutter. Does any one know about PCM's. The reason I ask is . I drive a 98 xj w/manual trans and my wife drives a 99 xj w/manual trans. Can I switch PCM's without a problem for testing purposes, or will this give me more problems. I have already changed . Cap,rotor,plugs,wires, ign. coil, map sensor, throttle pos sensor, coolant temp sensor,intake air temp sensor, idle motor, and fuel pressure was a constant 45 psi . I am totally stumped. It only stumbles after completely cooled down overnite. And within the first mile or so it stumbles and then after that it is fine. Somebody please help.. I am about to fix it with a can of gas and a match. Thanks Brian

Have you checked for a dribbling fuel injector?

I did look at all of them and gave them all a little twist and did not see any seepage....

Dribbling does not refer to leaking around the o-ring seal to the manifold. It means dribbling as in not completely shutting off the fuel supply out of the spray nozzle on the injector.