01 T&C Transmission issues going through water

New transmission, was going about 45 in heavy rain. When I would push the gas alittle it started to clunk clunk clunk. Push the gas all the way and no problem. Put it in 3rd range and not nearly as bad. Just mainly in overdrive. Something is getting wet thats not supposed to and I have no ideal what. When I got home I popped the hood and could not see water in the engine compartment. The splash shields are on both sides of the wheel wells as well. PCM is new too. Anyone have any ideals? Thanks

Is your van "All Wheel Drive" (AWD)?? If so, I can tell you what the "clunk-clunk-clunk" is. Please respond.

No all wheel here, I did some checking and found one of the big wiring harnesses towards the bottom filled with water, don't think that was the issue but I drained it still had the issue. Tired of dealing with it I took it to the dealer. The battery was causing all my issues, engine managment, shifting, electrical, etc., and now that the battery is new, I have not had one problem with it. Thanks for your reply and sorry for not getting back sooner on this.