clunk/tap feeling under my feet.

[VXR]

Check the tranny mounts at the cross member - the bolts in mine backed out and the tranny was shifting left-right until they were replaced. It's hard to see that they're missing...note that this same problem has happened on other VXs...

-- John

I was going to say the same thing but when mine were loose I could only hear/feel at very slow speed not 25-60...

[Ldub]

Do any of you with the phantom noise have Trooper skid plates installed?

If so, check the right front where the front prop shaft intersects the front edge.
This plate is very poorly designed & crushes easily, allowing contact with the cap screw heads.

Just a long shot...

[LittleBeast]

I would check sway bar connections as well. At the a arms and on the frame mounts.