Some ideas on specific points, if you haven't yet worked this all out:
Notes I took from today:
- Rubbing sensation on inner heel (behind inside ankle); both left and right boot
- Lots of pressure when tightented down on top of left food; right food not as bad but still aches
- Bottom of left foot really sore immediately following run (front of arch, behind toes); right foot aches but not unbearable
- Toes okay (although big left toe is sore tonight), shins okay
Custom footbed. My bootfitter was StartHaus in Truckee (recommended from here).
The big issue is pain on my instep. Left boot is the worst but both are very noticeable if clamped down (see below, though).
Start Haus gives excellent service after the sale. And probably won't charge you much unless you do canting or something else fancy.
Rubbing sensations around heels are likely to be a product of movement, perhaps from boots being not closely fitting enough in some location, as opposed to being too tight. The shop could likely address this. It could also be technique-related.
Too much pressure on the instep isn't good. Most good skiers don't need to fasten the lower two buckles at all tight. Just one finger tight. It's the upper two buckles that you might want to crank down to take up any excess space and keep the cuffs fitting closely around the shins.
As to the pain in the bottom of the foot behind the toes--if it's not simply a matter of your instep being crunched down too much by the buckles--I'll put out a possibility that others may not have brought to your attention. This area is called the metatarsal arch. It's not the big arch that runs front to back. It's an arch in the bone structure, side to side, formed by the small bones in the forefoot. I had the same problem. Pain can be a result of the footbed providing an insufficient or inappropriate level of support for the metatarsal arch. Mark Elling discusses this in his excellent book, The All Mountain Skier. He calls it "da burning balls." It builds through the day, and it can be excruciating. The fix may be to add a bit of support in the footbed, toward the middle of the metatarsal arch. But a little goes a long way. It's very subtle, and it may take some fine tuning over time. But in my case, making the adjustment fixed me up a treat.