Most of the people I ride with get some element of foot pain, epecially the first run of the day which we just put down to not being relaxed and tensing up the foot.
I found I have a tendency to try controlling the board with my feet rather than the boot which give me cramps.
Best way I found was to have the bottom of the laces not too tight but the middle (heel) and top tight enough so that I can lean on the boots to turn with my foot still relaxed.
I allways slacken off my clipped-in foot a few notches in the lift queue to give it a break as well.
I have never really looked at my stance as a cause and found that to effect my knees more than feet.
Of course, if your boots are a bad fit and too loose/tight then that will obviously case you problems any way but, as long as they feel snug and confortable, I doubt they are the problem.