I got my DL when I first arrived in Thailand and did not have a 90 day report, I do not remember it causing any problems (but someone might correct me).
Do you have the international driving permit, as that made it very easy to apply.
Keith I think these are 2 of the easier questions and people have already answered them. The one that I was confused with was providing proof of who invited me, as I invited myself. I simply provided another picture of my passport because of this and it was approved, so don't be afraid of giving the same evidence several times. Good luck.
You could always book your return flight date for 90 days and buy a separate one way flight from Thailand to a neighboring country within the 60 day period (cheapest you can find as you will not actually use it).