You're trying to do too much in 12 days if one of your goals is not to be exhausted at the end of your trip.
I'd recommend adding time in Bangkok and Siem Reap and a third stop, and do this by eliminating either KUL or Phuket/Ko Samui. I'd cut out KUL.
The idea of swapping Phuket/Koh Samui for a destination such as Chiang Mai -- or Chiang Rai -- also is worthy of serious consideration.