Would I feel pain right now if I had cracks?
Borrow a tuning fork, ring it, and set it against the bone. If you have (a) stress crack(s), you'll know it.
Odds are good you don't.
Anyone have any suggestions as to what's causing the pain or stance suggestions to fix this?
In short, you're asking various tissues to endure a load for which they are not suited.
While a flat front binding is appropriate in some cases, those are in the minority.
Inboard canting at the back foot, in combination with a flat front, tends to twist the board on the heelside turn, and this may be part of your problem.
As stands, the mechanical advantage favors your board on the heelside turn, so the loads of that turn are expressed against the side of your front leg, rather than through the soles of your feet.
Your boot cuff should not be considered a lever of activation, rather a lever of stabilization.
I'd like to work with the equipment I have.
"Hey Doc, it hurts; but only when I do this."
"Well... Stop doing that..."
Resign yourself to the possibility that you may not be able to find resolution with your present bindings. The TD 1 is mighty fine, but not without the ability to fine tune the canting and lifting
If you are on a budget, and mechanically competent, you do have options.
At the very least though, this will involve another 3 degree base disc, some longer fasteners, and a bit of creativity.
PM me your email, and I'll forward additional information.