Remember if you arrive at a land crossing into thailand you'll only get 15 days stamp.
I occasionally take a car to Poi Pet, walk over the border (do the visa on line beforehand) and haggle a 30$ cab to Siem Reap. Then just fly one way with Bangkok Air back to BKK. There's bnot much to choose from ex pattaya in terms of journey time. Personally I think the car is less hassle if you already have your cambo visa.
Kathmandu is very third world. Last time I went they do a visa on arrival. Interesting enough for a couple of days, but still a longish flight for a weekend. If you're splurging the Dwarikas Hotel is a nice retreat away from the dust, dirt and smells. Otherwise find a nice guesthouse in Thamel. Thais get visa on arrival too. Personally I'd save Nepal for when you have a few weeks - easy to sort a tea house trek in the Annapurna or himalaya when you there. Just take some good walking boots and water steri tabs.
Unless Air Asia are bloody cheap into KL you might do better on Lufthansa or Thai into KLIA. Just a thought. Lots of good 4/5 star hotels with OK pools to crash next to for 3000 baht a night. If first time I'd head to Bukit Bintang, KLCC is a bit sterile, and there's plenty of nice bars and restaurants nearby.
I'm going to do visa trip to Penang next week. Never much liked the Butlins type resorts there so plan to stay in Georgetown for first time - looks like there's some nice enough heritage type guesthouses for 60-80 us a night. There's also (I hear) a 50m outdoor pool nearby that only costs 3-4 ringitt so some laps in the sun should sort me out ready for a few beers in the evening.
Look forward to hearing where you decide, with long TD thread including at least 6 pics of the inflight meal etc.