I've been having the same problem as KDriscoll (recent post) for 3 years (Ken I know how you feel).
The pain starts as an ache in the instep and radiates to the outer edge of the foot, where it feels like severe burning/pain, about half way between my toes and heel. It also becomes so bad after 5-10 minutes of skiing that I have to stop and take off my boot, after a few minutes it's fine and the process starts again.
I've seen sports physios, podiatrists, had arch supports, ankle supports, full orthotics, heal lifters, personalised heat moulded ski boot orthotics and nothing has worked. I too have Head boots as I was told that they are simply a better, more comfortable fit for a wider foot.
I do have medium pronation on both feet (flat feet) and ended up seeing an ankle and foot surgeon (2010-11). Since then have had nerve conduction studies, x-rays, MRIs, ultra-sounds scans and Steroid shots and when none of these worked, in March '11 finally had Surgery; a Tarsal Tunnel Decompression in my right (worst foot).
The surgery site is healed now and went to a indoor snow centre a few days ago, full of excitement as the ski season is fast approaching here in Europe......and AARGGHHH......It's still the same incredible pain in the outside edge of my foot....
I have also read that if Boot fit problems occur as the foot is forced to pronate (flatten) causing pressure of the foot against the boot shell. Typically this pressure occurs at the base of the little toe. Also, because the foot is flexible, the muscles and tendons of the foot are "fighting back" to resist the pronatory movement (flattening of the arch) causing aching in the arch and mid-foot.
Apart from the obvious, give up skiing which is not going to happen, I'm at a total loss as to what to do now....CAN ANYONE HELP PLEASE?????