2011FordFusion

I joined this page because i am having a problem with my 2011 ford fusion (2.5 SE) So i am definitely not a mechanic, but i do know how to turn a wrench. I swapped the transmission on my fusion after it sat for about 4 months. After i put everything back together and hooked all the wiring up i tried to start the car. everything turned on but when i went to start it, the theft icon came on and on the dash it said "--- miles to go till E". it would not turn over or anything like the computer is telling the car not to start. I did a bit of research and did not find much. I did find out that when it says "--- miles to E" that is fords way of telling you that the PCM is not communicating with the rest off the car, or there is a bad ground. i cleaned a few grounds and got rid of all the paint to make sure it was an actual good ground and nothing changed. i saw many little things to do with the key to get rid of the anti theft but none of them work. So i am stuck with the anti theft lock on and what i think something to do with the PCM. Can anyone help?