I take it you tried erase and program and not add additional keys??? Have to do erase old keys. I'm Ford tech and encountered this before. so either your trying to add additional keys, or you have a problem with your pats transceiver circuit not allowing keys to be programmed. Since it's pretty simple, plug in old pcm and c if you can erase and program keys, and if you cant then you know it's pats issue.p1260 is just a code saying no keys programmed that tried to start the car.

 You have to program the PCM to the truck. The VIN is the handshake. Perform a new PCM installation, then run the PATS function.You will probably need two keys to complete the process. Have a great day.  

 Oh yes overlooked that i just assumed he did the first step a pmi but that is probably the case here then.

I guess you had all the remote start crap disconnected, and  truck wires reconnected to the original configuration? Could need a new lock transceiver after all.

 you will need to keys. after programming keys log in to pats again and do a parameter reset, not to the IC, you did not replace the instrument cluster, when prompted on the parameter reset choose pcm not I C. check the data log on pcm it will tell you how many keys are programmed, if none you have another isuue, if 1 key is programmed then one of your keys is bad, if 2 keys are programmed then is your parameter reset. remember to choose pcm and not IC. the IC is in charge of pats but you did not replace it. also when going back to the previous pcm programming and parameter reset most be done as well. good luck     

 also programming pats keys is possible even without having to rewrite the vin to the pcm, in this case flashing it. the only problem you will have a vin mismatch code and the abs light on. not your case since your pcm was flashed, hopefully they wrote the correct calibration to it, the vin alone is not enough. if the above procedure does not work for you I guarantee a bad tool, get the ford ids and it will work flawlessly.