We did this trip in reverse order about 15 years ago, Bangkok, Koh Samui, Chiang Mai, and then 3 days in Tokyo on the way back.
We were dirt poor grad students on our honeymoon, so we stayed in very basic accommodations and were on a budget.
But some of the stuff that we loved:
Scuba diving with whale sharks off of Koh Tao
Just wandered Koh Samui, saw the mummified monk. Koh Samui had a lot of Russian tourists, sort of like their Cancun. Not as party as ****et.
In Chiang Mai, we went to a culinary school for a day where we shopped in the markets and then cooked a few meals. That was an incredible experience.
The best meal I think I've ever had was at a little alley restaurant/cart. Two meals and two sodas and she held up 6 fingers. I thought she meant 600 baht and she was surprised and gave 540 back, 60 baht for lunch, $2.
We were going to go the elephant sanctuary Patara elephant sanctuary, but had to cancel that and ended up taking a hot air balloon which was a lifetime memory.
I don't remember much specifically about where we ate, etc. But we had an incredible time.
Edit. In Tokyo a couple really memorable things were: we went to the sumo championship which was really damned cool and we waited in line crazy early in the morning to have omakase sushi breakfast at Sushi Dai in the Tsukiji fish market. We did it in January and it was like 18 degrees. Probably a lot more fun to wait three hours at 3am in the summer. Absolutely bucket list experience.