Can you help me diagnose what is causing heavy shimmy upon braking?

My '98 4Runner 2WD with about 50K miles is vibrating heavily when braking
at highway speeds. It does not vibrate under any other conditions.

The cause is perplexing me.
Here is all that I know.

- The 2WD 4Runner is not equipped with ABS braking
- The four wheel alignment was done about two years ago
- New tires about a year ago were dynamically balanced when mounted
- The front rotors are smooth with only a single circular scratch in one
- That one rotor scratch is so thin a pen tip won't even catch on it
- The rotors are 0.860 & 0.855 inches thick (min=0.787 inches)
- The pads are about 1/4 inch thick (minimum = 0.039 inches)
- Disk runout was 0.002 & 0.0025 inches (min=0.0028 inches)
- The rear brake drums were not checked
- I did not perform any other tests as I don't know of any other tests

One wierd thing happened while checking disk runout. There was a repeatable
half of a thousanth of an inch "blip" when I rotated the rotors. It was
always in the same spot on the passenger side rotor. I could hear a
scratching sound for a second when I saw the blip on the dial guage. Funny
thing was I could not see any "dent" or imperfection in the rotor at that
point. This rotor wasn't even the scratched rotor so it looked nearly brand
new (even after 50K miles).

Other than that blip, everything seemed normal.

At first I checked runout without removing the pads and without putting the
lug nuts on but the runout was changing until I realized the rotors were
only held on by the lug nuts so I removed the pads and jammed a screwdriver
into the rotor fins so I could torque down (83 foot pounds) the lug nuts
with a washer to prevent cracking the disks.

Do you have any idea what test to run to determine the cause of vibration?

Stu