FWIW, I swapped my Bonne mid controls with a guy for his Thrux rearsets. The Thrux owner and I swapped everything on the right (brake) side from the brakeline forward (disconnected at the caliper). Brakelight switch, master cylinder, reservoir, the whole enchilada. Took about 20 minutes to take it off and about the same to reinstall. Everything on the right side swapped on and fit fine. The left side (shifter) was even easier to remove/reinstall, and everything worked great installing my Bonne mids on the Thrux. HOWEVER, on the Bonne, the Thrux shift linkage comes into contact with the Bonne exhaust, forcing the shift lever to be tilted way up in order to work. The linkage can be adjusted for smooth shifting, but the actual shifter peg is way too high (with my foot comfortably on the footpeg, the shifter peg is approx 1" above the toe of my boot).
Obvious solutions include going to Thruxton headers/mufflers in order to gain the clearance; evidently Thruxton headers mount significantly lower on the frame than Bonneville headers, providing mucho clearance on both sides. Another fairly simple solution is to engineer an extension onto the shift linkage, effectively lowering the shifter peg about 3". Since I really like my ceramic coated headers and Epco mufflers, I'm going to pursue the latter solution with my meagre machining skills and try to avoid having it look too home-made.