Hmm 9 weeks was peak tiredness and nausea for me - sorry. Eat little and often, plain food/carbs - carry a packet of crackers with you at all times, and plenty of fluids.
Also you may be knackered especially early afternoon so build in siesta time. For example if you are off to Angkor Wat then do two trips morning and late afternoon each day, rather than reckoning on one long day (the temples are far nicer early and late anyway, less crowded and more atmospheric). Same advice if going to see the orang utans (from memory the trips tend to be morning and evening anyway).
Diving is off the cards but snorkelling is fine so choose beaches that have coral close to shore. There is a lovely island off Borneo close to the orang utan reserves, where there are baby turtle hatcheries - can't remember its name but I can look it up if you are interested. Pricey though, Cambodia is probably better beach wise.
Shell out for decent transport - road travel in both countries is slow and unpredictable (and not very safe) so consider internal flights (v cheap and modern in borneo at least) or trains where available.
I can't remember the malaria situation - I think we took Malarone, no idea if this is safe in pregnancy, but do check obviously!!
Good luck - I do think the key is not to try to do too much, DH and I did a similar trip and with hindsight we crammed too much in (and I wasn't pregnant!)