I'm closing the loop on this one with my final solution. In the end I found that the problem was likely two-fold. Initially the bad vibrations were warped rotors from stuck calipers. The second time I had bad vibes might have been rotors, but I now suspect it was a loose wheel bearing. So I was tired with chasing this gremlin and decided to fix this damn thing. I put the truck up on 4 jack stands pulled the wheels and started is and put into Drive. Found that the rear rotors were dragging pretty bad and one was very warped. The calipers were shot so I bought OEM front and rear rotors, new rear calipers, new SS brake lines and went to work.
The hardest part of the whole job was having to replace two hardlines because the factory torqued them so hard it flared the brake line nut so it wouldn't go into the new lines. Oh and getting brake fluid all over the place. In the end the problem is solved. So it was bad front rotors caused by bad front calipers, then bad rear rotors caused by bad calipers. In between I replaced two sets of probably good rotors because the nuts backed off the wheel bearings.
Now it's totally smooth, no pulsing. All I had to do it replace everything.