REP-LPQ routes through BKK, so it costs you two $80 coupons. You may want to consider Thai's nonstop CNX-LPQ flight to save time and perhaps a little money. (Ask a Bangkok or Chiang Mai travel agent about the one-way fares. There's a recommended Asian travel agents thread in this forum.) You could fly BKK-CNX ($50) on Bangkok; CNX-LPQ ($???) on Thai; and LPQ-BKK-REP ($160), REP-BKK ($80), BKK-USM ($50), and USM-BKK ($50) on Bangkok. (Make sure that an open jaw is permitted on the Discovery Airpass.)
Your itinerary is a bit ambitious: lots of flying and trips to and from airports. I suggest that you ditch one destination, spending four days each in three destinations (plus Bangkok).
You'll need three days in Siem Reap to cover the major Angkor sites, and it's a good idea to have an extra day to wander around the town, relax, and, perhaps, visit the lake village. If you're not accustomed to heat and humidity, I highly recommend booking a hotel or guest house with a pool.
Four days will be OK for Luang Prabang; four months would be better. Its major sites are somewhat underwhelming, but the town is charming and intriguing -- one of those laze-about-and-soak-in-the-unique-atmosphere locales.
Siem Reap and Luang Prabang are definitely go-now destinations: Angkor Park has already been overrun by tour groups (and it's only going to get worse), and Luang Prabang is at the cusp of being discovered by the masses, with (daily?) flights from Hong Kong in the works.
Be sure to check out the good, recent thread on Siem Reap and Luang Prabang in the Trip Reports forum.