Seems you and me are in the same boat/boot.
Your feet need a certain shell size. I assume you selected the most smallest possible for you and you had the toes punched in order to have these pain free.
Because of the low volume feet you probably could use a Bontex insole shim (www.tognar.com) to get rid of some of that extra volume in your shell. Next would be a custom footbed, which you probably also already have. Hmm.
Make sure your boot cuff alignment is correct.
Take the liner out, put the footbed into the shell and put your feet on the (centered) footbeds into the boot shell. Check if your shin and calvs are equally align in the cuff area of the boot shell.
Never over buckle! I agree with Bob. Over buckling creates issues. As bob said, buckle just tight enough to keep it from popping open and add a booster strap as well.
Your Indy’s, do you ride em with the hard or soft spring? Soft would probably be better for you.
I think you need to see a really good/creative boot fitter. You might want to check out a foam-injected liner (what I did). But even with them you may need some additional work done (extra padding build up around the area between the ankle where the foam pocket ends and the calf, some stuff to push you more into the heel pocket of the shell…).
Remember, ride hard when the snow is soft, ride soft (er) when the snow is hard!
I recommend taking Arnica (homeopathic), this stuff really helps a lot to let you heal fast (was recommended by someone here in the forum to me).
I believe in it! If it’s really bad and does not get better in a few days have it checked out, you never know.
All just my own experience.
Ray