Ok, I checked lines, front suspension components, and lug nuts. I was just about to take it somewhere out of frustration, but decided to check runout with my cheap dial indicator. Was fairly certain the problem is in the rear, so checked the rear drivers-side runout - ~.002 (new rotor). No problem there. Moved over to passenger side - ~.012 (also new rotor). Probably within spec, but much higher than the other side. I decided to try to index the rotor before changing it, which helped a little according to the dial indicator, but the pulsing was still just as bad. I then took off the brand new rotor and put one of the old ones back on. Runout was now ~.005, and pulsing was MUCH less evident. Still perceptible, but not nearly as bad.

Might get the "bad" new rotor turned, and the other old one just to see if I can get all the pulsing out. I assume it could also be an issue with the way the rotor sits in the axle, though there is little I could do about that (did sand all the rust spots off, just in case).

Bob