Pcm was stolen at repair shop. put re-maned one and had it programed to vehicle.now it wont stay running and has a miss. ran like new prior,,had trans replaced

It's the anti-theft system . (SECURITY ) Keeps vehicle from being stolen !
Important: If the wrong ignition key is used in an attempt to start the vehicle, a Data Trouble Code (DTC) will be set and the Body Control Module (BCM) will not send a fuel enable or starter enable message to the Powertrain Control Module (PCM) for three minutes even if the correct ignition is used.
The Pass-Key II?® Theft Deterrent system prevents vehicle theft by disabling the starter motor and fuel system. If the Body Control Module (BCM) dose not identify the use of the correct ignition key to start the vehicle, the (BCM) will communicate a message to the Powertrain Control Module (PCM) which will disable the crank relay and fuel delivery to the engine.
When the (BCM) identifies the use of the correct ignition key (resistor pellet) to start the vehicle, the (BCM) will send a fuel enable and starter enable message to the (PCM) which will allow the vehicle to start.
Your best bet would be have it towed to a qualified repair shop !

THE PCM IS VERY DELICATE IF NOT HANDLED PROPERLY CAN DESTROY IT. THEY ARE VERY STATIC SENSTIVE THEY SHOULD ONLY BE REMOVED AND INSTALLED WITH ANTI STATIC GLOVES AND ONLY PUT ON ANTI STATIC SURFACE WHILE CHANGING OUT AND INSTALLING

Given the vehicle,age & all the terrible
transaxle problems on a windstar & vehicle
it replaced

Your transaxle has failed

Having once owned a trans repair shop

Get rid of it & never buy another van type
vehicle,any brand

I am assuming that the vehicle ran prior to getting the transmission repaired. If so you should not need any new keys and the computer should be good. The shop doing the work has obviously done something wrong. If it did not run prior to taking it in for the tranny then it could be many things. Hard to tell without seeing the vehicle. If it was running prior to the work and it's still in their hands I would suggest you get it away from them ASAP.

check out the neutral saftey switch on trans, if its reporting unknown gear on scanner while moving t bar it wont know what gear to be in and give you similar problems, also has oil been leaking into switch before?

Have you checked the distributor or coils? Maybe your rotor is not turning. It could be so many things.

That sounds exactly like a problem with the PCM. (Powertrain Control Module)

I have heard of aftermarket stereos and even the passenger side air-bag switch causing similar problems, and a "No Bus" message means that the PCM is not communicating with certain modules, and the dash lights and gauges can become erratic and the vehicle performance will be affected.

The next time that the vehicle acts up try wiggling the connector at the PCM and see if it makes any difference, and also you can dis-connect the battery, and dis-connect the wiring connector to the PCM for three minutes and then re-connect the PCM and then the battery and see how the truck runs, if it changes how the vehicle runs and the dash lights and gauges are normal with no "No Bus" message, then you will need to replace that PCM.

that pcm needs reprograming, you just cant buy one and put it in, the new computer needs to be programed or the car wont run, it might start but it will die out,have the pcm programed and if that was your problem the car should run. hope this helps.

did you use the existing ecm or the one that came on the new motor. probably need to program the wcm. transfer secret key also. sounds like the problem to me. if the vin number in the ecm/pcm/wcm dont match the truck wont stay running