With these priorities, it makes sense to leave KUL and SIN out of the October picture, yes.

IMO, it is not worth the time, extra cost, and visa expense to go to Vietnam for just a couple of days or so. It really adds a layer of complexity. Saigon just ain't that much of a highlight of SE Asia. Save it for a future trip to Vietnam, and plan to spend 2-3 weeks just for that country. Now that you've got your priorities Phuket (or Krabi) and Siem Reap/Angkor, just build on those--there is no shortage of interesting places to go in either country. You only have 12 days. For your award tickets, check to see what gateways are available in Cambodia (I hold no hope for REP but is PNH possible?). Then we'll build you a cost/time effective way to get from one area to the other.