I posted something yesterday but received some more details today so maybe with these details this will make more sense...My 05 350z was on a street that flooded, i went out to start my car it was dead so i got it jumped and noticed that when i put it into drive it "kicked" into gear real hard. Driving the first 10-15 mph is real sluggish then it drives fine. My check engine light came on and my A/T light as well. Called my insurance to put a claim in because of the water damage. The first place that looked at it had code p1065, and recommended that I send it to a Nissan Dealership so that it could be better evaluated. Once there the code no longer came up, a different code for the evap canister popped up (which wouldn't be causing any of these issues or be from water). However, the transmission problem is still there...Do you think that the ECM (p1065 code) could of shorted something out and caused a problem with the transmission? I never had any problems with the vehicle its a 2005 with 54k miles on it. Water was a little above floorboard high and i hit a deep puddle on the way home (roads suck around where I live).

 

The water most likely cause issues. Sounds like you are going in the right direction with your insurance. Why not take it to a nissan dealer as they will know the electrical system the best and you can use their estimate as a baseline for the repair cost for you insurance.