MUSTANG SPUTTERING AND LOSS OF ACCELERATION AT LOW RPMS

My car was being fixed at the body shop they decided to spray underneath the hood!!! The entire K&N air filter was waterlogged. Later that day the check engine light came on and read that read number 6 spark plugged was blown etc. I replaced the filter and also replaced the spark plugs + cleaned and dried out the throttle body. I left the hood open in the sun for the day. The check engine light is no longer on and the problems seem to have gotten a little better. HOWEVER STILL after letting off the clutch it shakes and sputters and continues to shake until the RPMS get above 2,000 to 3,000. What else could be causing this. ALL SUGGESTIONS WELCOME PLEASE. Im thinking i should have replaced the COIL PACKS. PLEASE HELP.
 
Clean the MAF.

Any DTC codes (check engine)? If yes, please post the full codes.

I think likely that the MAF is still wet or has been damaged by water. Clean the MAF with cleaner made for the job. Let air dry. If no improvement, some consideration should be given to replacement (further tests will need an ODB2 scanner).
 
Original Code

Original code before I changed the spark plugs was P0306.
Probable cause
aa1. Ignition system fault-spark plug (s), ignition wires, coil.
aa2. Vaccum leak.
aa3. Injector Fault
aa4. high or low fuel pressure.

Whats most likely and least likely and how should i go about fixing this.
 
Wet COP

IMO, it is silly to think that the problem is a bad spark plug. Consider that the problem began AFTER the engine was subjected to a wetting event. It is far more likely there is water in the spark plug wells, water in the COP boot, or water in the COP electrical connection.

Normally, ignition problems get WORSE as RPM's increase. But since you did not post the actual DTC codes, this left me to guess. Lesson. Post all of the details for quickest results.

Consider replacing the #6 COP or swapping with another cylinder and see if the DTC follows the COP.