Fun little mud puddle I go play around in every now and then seems to make my little jeep run bad. Runs fine in the mud and littler puddles. Once I go through deep one.(half way up doors, stock lift and tires) makes it run like ****. Water in exhaust or dist cap or what???

If it dosent throw a code it is water in the cap if it dose throw a code it could be the connection

How could I protect from getting water in there?

On the cap put some silicone around it and your sensors connections put some grease on them

And is it alright to use a pressure washer on the eng. Compartment? Being cautious of course. Would like it clean to fix the problem.

I do mine all the time I have had only 2 problems got a seniors connect wet and water in the cap so yes its fine

Might do it with engine running. Any problems with that that should I should be concerned about?

No u have to do it with it running