+1 on those recommending direct BKK-REP. The BangkokAir multi-segment promo sounds fantastic and would allow you to see a bit more than you might have otherwise planned. If still available next time I am in BKK I would certainly look into using it.

However, I have considerable respect for how budget and time often conflict. If you have more time than money, there are cheap ways of travel between PHN and REP, including boat.

That said - get to REP as quickly as possible. I can not properly convey how lovely the experience was for me and my travel companion. I do know, however, that the city is changing and it will lose a lot of its charm and, dare I say, innocence, as tourism increases.

My only additional advice is to recommend taking some simple face masks, ala Tokyo Traffic Police, if dust bothers you significantly. If - hell, when, I return I plan to use them while riding in the Tuk-Tuks, but not while wondering the streets or the temples.

Safe travels!