NEED HELP!! Failsafe & check AdvanceTrac

[NotMine]

I have a friend of mine's 05 explorer 4.0 RWD. All of the timing chain guides broke apart a couple years ago so he parked it and tried to do it himself. I got it a month ago and the intake, timing cover, a couple of the front guides, and one valve cover was off. Problems started while trying to remove the motor. we couldn't turn the engine a complete cycle before it stopped, therefore couldn't remove torque converter bolts. we removed the engine and trans. disassembled engine and find it to be rust in two cylinders that was stopping it from turning over. Put new chains, guides, all new gaskets. bought tool to time it correctly and reassembled engine and attached trans. installed into truck, but then realized the intake and throttle body were not in the back with all of the spare parts. found one on Craigslist (the little plug or whatever it is on top of tb is broke off). Filled all of the fluids (except trans) and started. it immediately went into Failsafe mode and said check trans and Advancetrac. we then filled the trans (pain in the ass) until fluid came out of hole. cleared all of the codes and tried again. Same thing. There are a lot of codes. ( PC Solenoid a, OBD check incomplete, TAC forced idle, Throttle actuator stuck closed, PC solenoid b, pc solenoid c, pressure control solenoid a & b low, shift solenoid a & b & c & D Fault & electrical, torque converter clutch fault, TCC electrical fault, pressure control solenoid electrical) there were also codes in the ABS and for the gauge cluster. The only code that would erase when i tried was the one for the gauge cluster. all other codes it would say erase complete, but when i went right back into codes they would still be there. i am thinking that i missed a ground or something like that since it is so many codes and they wont go away, but cannot find any. only thing that i know for a fact that i did not bolt up was the plastic cover thing that the trans harness goes through that bolts to the head because it was a pain and i would have to take the intake back off. But that wouldn't ground to the bolt holes would it?? it will go into reverse what seems like normal, but when i put into drive it is very weak, like i can put my foot on the ground and stop it. and of course it wont rev up. have no throttle response whatsoever. ANY help at all would be awesome. i have never worked on anything that would go into fail safe mode. Thank you!!

 

[NotMine]

I finally got it to go out of fail safe mode by putting a new throttle body on it. do not need to reflash like ford says. But i still having problems with trans. All codes that could pop up are there (feels like). i have checked wiring and cannot find a problem. have also located any ground that i could and made sure connection. anyone had this problem before??