we already have the long haul flights all figured out. Our current itinerary is (this is going to need a lot of brushing up as we're still deciding on flights within asia)...
Arrive in Bangkok May 30th
A couple of days in Bangkok, mainly to rejuvenate ourselves after the flight
Travel up to Chiang Mai probably by overnight train (we're on a pretty tight budget fyi)
Chiang Mai for 4-5 days?
Fly to Luang Prabang (probably on Lao airlines. I know you can do it on the Discovery pass but the lao flight itself is cheaper. although I am slightly worried about getting one of those chinese planes)
Luang Prabang for 4-5 days
Here's where we run into some trouble. When we were originally planning the trip there was a direct flight from LP to Siem Reap. That has now been cancelled so we're thinking go back to Bangkok and actually sightsee then (this was originally planned for the beginning of the trip but I thought this way, it would seem less like backtracking)
Then off to Siem Reap (probably using discovery pass for the LP-BKK-SR flight)
Siem Reap for 4-5 days?
Back to BKK (I hate this backtracking but I can't think of a better way)
And then down to Samui (I really liked your idea of having that as our home island base) for 5-6 days of relaxation
Return to BKK for another few days of shopping / sight seeing
Fly home to Chicago on June 29th.

I am currently researching the cheapest ways to travel to each of these destinations. If you have any tips on the cheapest way to Samui (I believe only Bangkok Air flies there correct?) that would be great.

We're also looking to find cheap accomodation although, as you said, we'r e not overly worried about that. We want to have a place booked for when we arrive in Bangkok but that's our main goal.

Sorry for the ridiculously long post. JamesA, you have been amazingly helpful with all of my questions. I really really appreciate it. Khop Khun Mak Kha!