Motor has 54k on it from a 08 was installed in my 06 truck 3 months ago, runs GREAT, intake manifold and TB carried over from old motor.

Dead battery swapped, got the low idle code, time to clean the TB, 2nd time I've done this on this truck. Oddly enough the truck runs fine even with the check engine light.

Pull it all apart clean the TB and the lower portion as well, all new gaskets OEM, fire it up drive 10 miles, drives GREAT, buy some Redline fuel injector cleaner, put it in (had a full tank of gas). Drive 2 miles park for about 20-30 minutes, soon as I get back in and drive off, truck is starting to idle rough, motor is visibly shaking I can feel it in the seats.

Car won't throw any codes, spark plugs are new installed with the new motor swap, COP only have 54k along with injectors.

TPS and EGR are original (140k).

I changed the fuel filter, cleaned the MAF checked everything twice, unplugged the battery again, no change.

Guess I should start unplugging the injectors one by one and listen for a change in idle, probably do the COP as well tomorrow.

My scanner also has the Ford KOEO AND KEOR tests I ran those and it through no codes.