I've been taking Knott's advice and so far it's working out great.

Foot exercises (also hip exercises) - yoga, plus some isolation exercises.

Ditched the custom orthotics (and all other medial arch support).

Metatarsal domes in my running shoes for the time being, but not in my other shoes. I foresee the day when I won't need those - I can walk and stand for hours in flat shoes now - but I can't run without them, yet. (Actually it's been months since I tried, but I'm not changing anything until after my second marathon, October 17.)

Shoes long enough for my toes (and also wide enough for my forefeet, but that's not necessarily related).

General postural work to correct the forward lean that resulted from the unstable base. (yoga again, especially the backbends, and just really being aware of my posture as often as I can).

None of this is an overnight miracle, but I expected it to take some time and work. Learning that my body can heal itself if I learn to stop hurting it ... priceless.