Hey Foxy,
Congratulations! This is terrific!
I don’t know about all this tracking and measuring stuff...sounds a little sketchy to me.
I kinda think you might have answered your own question at least partially on the workout/muscle thing. It sounds like you’ve been working out really hard and doing a lot of things with your lower body and yet it gets smaller. We could speculate about your fast vs slow twitch fibers and all of that, but a couple of things stand out to me; you are vegan or at least close to it, so I think it would be hard for you to get the really large amounts of protein that would accompany the extra heavy slower work of gaining much bulk without resorting to isolates. Of course you may be doing HIIT intervals, but still the dietary stuff...hmm, well, I would tend towards experimenting

, you have your current thigh measurements, why not go for the workout you want and check the measurements again in two or three months and see how your body is reacting? Then just adjust the workout accordingly.
Are you meeting your goals as to how you want to perform in endurance, strength, and flexibility? I don’t know your end point, but it sounds like you are paying attention and trying things, and that will lead you to your own answers.
Food tolerance is sure an interesting development for me also, so, I hear where you’re coming from. Who knew wheat could be a sleep aid?? Trial and error....at least it’s not boring, lol.
P.S. cashew butter is brilliant stuff