2005 GT 4.6 pcm/wiring? Issues please help!

Okay I bought a 05 roush 5 speed 4.6 about 2 maybe 3 weeks ago not it was wrecked in the front in of course one of the first things I fixed everything else seemed amazing other then a fan not wanting to kick on but heck that’s fixed now too anywho it’s back to normal other then some paint work but I drove it to work for about a week it’s a new car so I didn’t want to get in it or anything to hard but one time so it drove wonderful I was starting to fall in love with the car then one Friday afternoon it went to fail safe mode and wouldn’t start easy and when it did it was real choppy the dead I replaced the Trottle body so it stays started now but still goes in safe mode after so long I’ve checked plugs cleans plugs I’ve checked almost 85% of the wiring I’m at a lost again I can start and drive but no telling how far and how long and I half to use a $800 dollar code readers to clear the codes to get it back out of safe mode

PPLEASE HELP IF IT WAS A 99-04 neweadge I would have it under control.