Just got back form the Doctors. Good news is no UTI (he did a test in house for us). The Dr said cloudy urine in the morning is normal. When they have a really long sleep (DS sleeps roughly 9pm -9am) sediment can build up and it is flushed out in the morning. As long as it goes clear during the day (he had a nice clear pee for the Dr) then it's nothing to worry about.

The reason he is grabbing himself and saying his penis hurts is he has a mild infection at the tip of his penis just under the foreskin. It's very mild but enough to cause discomfort and combined with the sore bum (it's been so hot and damp here he has a bit of Thrush in there) is maybe distracting him enough to miss the cue that he has to pee until too late. I guess toilet training set backs are pretty normal too, he was just doing so well I thought his accident days were behind him. We're to put a bit of polysporin on the tip of his penis and some ketoconazole on his bum and he should be more comfortable in no time. Once his infection and Thrush clear up, hopefully his accidents will stop too.

Thanks for all your help!