I've done some searching and there are plenty of other cases where the source of the front end 'hop' was located at the rear of the bike. From rear sprockets that were out of round, chains with tight spots, swingarm bushings, worn out rear shocks, too aggressive rear shocks, wrong fork oil, clogged orifices in the fork dampeners, misaligned forks, bent triple trees, cracked triple trees, steering bearings too tight, steering bearings too loose, steering bearing races notched, flat spots on tires, flat spots on rims, tubeless type tires not seated correctly, bits of inner tube trapped under tire bead, a variety of spoked wheel specific issues, wheel bearing issues, axle issues, spacer issues, and frame issues.
Since your most apparent mod is the rear struts, I'm thinking that your front end is reacting to the change in resonant frequency they made by exhibiting this vibration in the speed range you're noticing it. Fork oil is where my search points me. Have you changed it or is it old and original? Maybe go heavier or lighter than what's in there now... if you've changed it.
And be sure your forks are nicely aligned too, there's a Hondaman trick out there somewhere that roadracers used to align the forks, something about loosening certain things up and pogo-ing the front end up and down with the tire on the ground, then re-tighten the loosened things in a particular order... maybe he'll chime in...
Good Luck.
-A