I have a '95 LE V-6, which has discs brakes all around (but no ABS) and a 5-speed, total mileage
about 128,000. Having experienced substantial vibrations at highway speeds, I have done
the following:

1) replaced tires
2) replaced steel wheels with alloy wheels (torque spec is 62 ft-lbs)
3) replaced front rotors and pads with stock items
4) replaced rear rotors and pads with stock items

Vibrations were almost completely eliminated, but...

On a 1000 mile trip (following about 400 miles of city driving after completing #4 above), the car started strong vibrations on braking from highway speeds 900 miles into the trip. These vibrations are only
noticed on moderate to hard braking, not while driving. These vibrations were not felt so much in the steering wheel, but more in the pedal and in the of my pants. Vibrations diminished significantly below 35 mph, but when coming to a complete stop, it feels as though the brakes are pulsing, though not at all like ABS. I noticed on the rear discs a narrow band close to the hub where the pads were not fully engaging
the discs and a slight rust film developing. As a result, I replaced first one rear caliper (driver side)
and then the other (passenger side). The pads are now fully engaging, but...

The vibration/shudder, although diminished, remains.

Suggestions?