You are SOOO psyched!
I was in Bangkok, S. Laos (4000 islands region of Mekong), S. Vietnam (Ho Chi Minh and Cantho) and Siem Riep, Cambodia for 3 weeks in January of 2007. I am so envious of your 3 months!! My brother and his wife just moved to Hanoi, so I'm looking forward to a a visit to N Vietnam and N Laos sometime soon! I was recovering from shoulder surgery and didn't paddle (except sit on top kayaking on the Mekong in Laos, which was AWESOME). From the little I know, I'd say DO NOT MISS
Angkor Wat/Siem Riep and Hanoi/ Halong Bay. Angkor area was perhaps the most amazing sight I've ever seen. I also loved going to 4000 Islands (I think we were on Don Khon island) - super beautiful, fun, with some amenities yet a very rural sleepy place. Cantho was great for it's floating markets. In Bangkok eat dinner at Cabbages and Condoms.
Re: boating, I don't have much to add to what you already know. But in 2007 the Banff Mtn Film fest had a film that I'd highly recommend seeing. I'm a freshwater ecologist so it was particularly interesting to me, but just and amazing kayaking feat and environmentally enlightening too:
Exploring The Mother of Waters
(Australia/2006/45 min) The first complete navigation of the Mekong River, from its source in Tibet to the South China Sea.
I have some photos here if you're interested:
Feel free to email if you'd like: riverbioatyahoo