At first , I thought your problem was a stuck caliper, which only becomes stuck after heating up for a while.Shaking would be caused by the caliper grabbing a warped rotor.However, if this were true, when you experience your problem ,your wheel would be hot to the touch,abnormally dusty, and you would feel your car holding back. I had a brake sticking problem on my Scirocco.Changed everything(pads and rotors, which were due, as well as calipers,master cylinder, lines,and finally, booster.). It was finally a pin hole in the booster diaphram. The pressure would build and brakes would stick more and more as I drove, from the diaphram not releasing.Let the car sit for 1/2 hr and cool down and brakes were fine again.
Although this may info doesn't solve your problem, hopefully it helps diagnose future problems for someone.
1987 190E 2.3L (Daily Driver)
1985 VW Scirocco (Mint-Summer)