Well, obviously it is rubbing on something, only part of the time. Next step, IMO, is to take things apart and find where it is rubbing (assuming you already tried changing the pads to be sure it's not a hard spot in the pads). That much cast iron gone, there has to be a very obvious mark, at least, on whatever it's rubbing against. For example, if it was hitting the trunnion somehow, there would be a corner of the trunnion worn away.
I can't really see in your photos ... is the rotor centered in the caliper with everything assembled? On the earlier TRs, the factory used shims between the caliper and its mounting bracket to center the caliper over the rotor. The shims have all gotten lost over the years (because they are a PITA to put back, even if you notice them falling out).
If you jack the car up, grab the tire at the top and bottom and try to wiggle it, can you feel any movement? If so, it may be that the wheel bearings are too loose. This is a common problem shortly after installing new felt seals, as many of the seals being sold are too thick and cause false clearance readings. Once the felt wears a bit, the bearings are too loose.
On my TR3A, I discovered that spindle itself was not round, where the inner race of the outer bearing fit. The race seemed to be a snug fit (as it should be), but the spindle was oval so the bearing was only snug on the front & back of the spindle. The result was that the race (and hence the wheel) could move up and down. That, combined with the normal flexing of the spindle under hard cornering, was enough to let the rotor hit something (I forget what offhand).