1995 Jeep Grand Cherokee with finicky overdrive

I have a 1995 jeep grand cherokee 8 cylinder that intermittently won't shift into overdrive. When this symptom occurs it will continue to "not shift into overdrive" until the jeep is shut down and restarted. It will "never" correct itself if the ignition key is not cycled off and then back on. The transmission has recently been overhauled by an aftermarket transmission specialist and the PCM has recently been replaced by a Jeep dealership. Both the dealership and the transmission shop believe that it is not the transmission. It does not have a TCM (it is a 46RH transmission) and there are no codes stored in the PCM. It does seem to be temperature related, as there is no consistency and the frequency is unpredictable; each time you start the car it will either decide to work or not, approximately 50% of the time. Also the O.D. Light/switch in the dashboard appears to be working correctly. The jeep has been at the shop more times than I can count over the past 6 months and am no closer to an answer. Since I don't believe in coincidences, there are two more symptoms that the jeep has that may be relevant to mention;

1. If I lock the electric doors (which automatically sets the factory alarm) the alarm may randomly go off hours later, unprovoked by anyone.

2. Intermittently I will comeback to my truck hours after leaving it and will find the brake lights on. If I pull up on the brake pedal gently the brake lights will go out.

Is it possible that the brake switch could cause all three symptoms? I have tried to pull up on the brake pedal when it won't shift into overdrive, but it does not alter the behavior. Can anyone help me to remedy this problem, I am out of patience with this problem?