Have had a breeze through this thread - interesting. Driving in to water is not something to do without thinking it through and should never be done at speed. 2ft of water should not really be a challenge for a D4, I believe they have a wading depth of 3ft and if you're careful you might go a bit deeper but not sure I would want to unless fully prepped for wading.
The symptoms described, a clicking/clonking when turning is classic CV joint. However, I would also suggest dropping the front diff oil, I believe D3 and D4 have the same front diff on the auto models. The front diffs can wear so I would be looking to make sure the front diff isn't eating itself. It is not difficult to drop the diff oil and replace but remember when filling, you have to put in the specified amount and not until oil dribbles out of the fill hole. I would also say, measure how much oil comes out of the front diff. you'll know if the diff is bad because of the swarf that will come out with the oil. If you're going to drop the diff oil, make sure you can open the fill plug before you remove the drain plug. HTH