02 s type 4.0 stumbles and chugs when first started then straightens out and is fine and Runs great.Brand new engine all new sensors no vacuum leaks. Was thinking it's the iac but not sure what tests to try to diagnose it.

 

Have you OBD'd it mine had something similar and it shows up as the Heater sensor on exhaust start-up. There's two, left and right sensors trying to get the emissions up to temperature for the engine to settle down on the revs. It also so I'm told has something to do with the Airmass intake sensor which causes it to hunt until its happy with operating temperature.

 

What are all the fuel trims like?

 

Any "engine fail safe mode " messages? I would get that for 5 seconds if I pull out without letting engine idle drop upon startup. Result: P1584 throttle body fault. After that, mine runs well after that.

 

What about the coils? New? Used? OEM Jag/Motorcraft or aftermarket? If used or aftermarket - get the coils tested.

 

I found water in the rear plug tube, causing a misfire. Any tips on sealing the coil cover so water doesn't get in.

 

The problem is water is dripping onto the engine bay (and coils) from the windshield cowl. There is a fix and I believe it's here on the forum somewhere and I also think there might be a youtube video of how to fix as well.

PS - that coil will need to be replaced and your going to have to seal the windshield cowl.

As a short term fix you could put some hylomar around the coil cover but water will eventually find its way into the spark plug well shorting out the coil.