I learned the following on the Lightning list from a Ford tech and it's worked for me.
After repairs, bring the engine to operating temp and shut off. Disconnect the battery for 5 minutes, no less, to drain the keep alive power in the PCM and clear all memory including codes. Then clean and connect the battery cables, make sure all accessories are off, and restart the engine. Bring the RPM up to 2500 in PARK and hold it there for 3 minutes, no less, let off the gas and let it idle down for another full minute.
This is supposed to help by shortening the adaptive "relearn" which normally takes up to 150 miles of normal starts and driving.
I would guess a manual trans would use neutral