OK so I have found a couple things.
First, when measured on the car, the front rotors have runout according to a dial gauge.
Second, in addition to the vibration while braking described above, I have had a shimmy in the front end of the car (while driving) at 40mph and up for as long as I have had issues with vibrating while braking. You can also feel a bit of a wobble right before the wheel returns to center when turning.
So I have naturally had my tires rebalanced several times to try to figure this out. Tires are balanced to "0" and road forced, so they are as good as they are going to get. Lately I have noticed that just taking the tire/wheel off the hub and putting it back on (no re-balancing) in influences how bad the shimmy is. So apparently the index position on the hub with respect to the lugs seems to influence this vibration? This makes little sense to me, does anyone have any insight into what this means? As far as I can tell the bearings seem OK (no play moving the wheel at 6-12 and 3-9). WTF?