Fail Safe Mode

My wife and I both have 2005 mustangs. Both are GT 4.6. Her battery died and would not start the car. I replaced the battery with a Optima red top and car started. Unfortunately the vehicle will only idle at this point and is in failsafe mode. I pulled the codes off of the computer and had a P2104 and a P2112. When I bought her car it did not have a stock ford throttle body on it. Someone had replaced the original throttlebody with an aftermarket unit and cold air intake. I have removed the throttlebody and cleaned and inspected. Cleared the codes. Both of the codes come right back.If someone could point me in the right direction other than Towing to a dealer would be greatly appreciated!

Tested Throttle bod with key on and it seemed to operate properly.(this is in failsafe mode) not sure of manufacture ie no name or part number stamped on unit anywhere. gears in stepper motor housing made of brass and show no sign of ware. ref v. to tps = 5.03. found signal on negative slop to be .1 v. lower that acceptable range(.61)....Attempted to adjust stop set screw and found it seized and damaged. swapped it out with working unit from my car.... and no more fail safe. cleared codes. wife happy but my 3v is silent. Not sure if I should repair part or just replace and if so with what. Stock 55 or b&k 62. how crucial is a tune and where can I learn more about process. Thank you for your response Sparta!