Dakota + Ivan = Trouble

Hello, I have a 96 Dakota (V6) that tangled with hurricane Ivan and I think it lost. It was submerged to just into the under dash fuse block :(. I cleaned and cleaned and cleaned, I also had the automatic transmission power flushed, I didn,t think the pepto bismol should be in there, It was running pretty good until last week and all of a sudden it seems to be running on 3 cyls. I thought its time has come so I did what a real dakota owner must do, I bought another 96 dakota (V8) but want to save my other. Checking the Dakota site I do not know which way to proceed, Any points short of changing all electrical would be appricated.