Hey, we travel like your plans regularly and I would firstly say that honestly we found Thailand to be considerably the best country in SEA to travel at the moment. We found the environment to be cleaner in the tourist spots as well as in cities. Also the quality of food better and clener. We had no issues on our last 10week trip around SEA including 7 weeks in Thailand. Perhaps we were lucky although we were more aware of what we ate. We ate in street food type places in Thailand but found those places too grubby in the other SEA countries we visited. It is worth taking probiotics I think starting before you go. The other option is to eat organic an apple most days including the core which is full of probiotics. (but not the seeds), and make some effort to eat healthily before you go. Avoid over processed fast food in the airports.
We take a filter bottle (eg Fill2pure) and filter tap water, saves wasting so many plastic bottles.
It is worth doing a bit of research on antibiotics in case you do get a bacterial infection (eg dysentery through food)
TBH with 7 weeks I am tempted to suggest Thailand only as it has such a variety of history, beaches (way the best), culture, and the most fun. Bkk then South then North Is a long way with so many fabulous stops with nice rooms and brekkie for around 1000-1500 baht even in beach areas.
Happy planning