The problem comes and goes?
Usually I think of a warped rotor as being always warped. In this case it does sound like deposits coming and going, although I wouldn't they could "come and go" quite so fast.
I have wondered about unbalanced wheels on my truck, as sometimes it'll have that shake around 55--and sometimes not. Depending upon how many turns I take, each of the wheels is in a different phase relative to the others. So sometimes I wonder if I have two wheels with slight imbalances that, once in a while, manage to hit the right frequency to shake.
No chance you have a loose lug, unbalanced tires, or just a cruddy road surface?
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Have you popped off the wheels and checked the pads? Big heavy truck, should be expected to use up brakes at a good clip. Might be a good time to check pad thickness. I don't know what pads you want to use, but The_Critic keyed me into the fact that Toyota dealerships may try to sell you a non-OEM lower-cost pad which may or may not be what you want to install.