Starter
Starter Rebuild / Repair
It appears the prime "suspect" in the dreaded "clunk" leading to twisted starter bolts (and also to starter clutch failure) is the improper use of the throttle (right hand!) when starting the bike. Advancing the throttle causes the TPS (throttle Positioning Sensor) to "misread" and to cause a kickback - the full power of which is directed at the flimsy internal structure of the starter. HERE are the proper starting techniques to avoid the problem.
It's also a good idea to take a good look at your starter to make sure the 2 bolts that hold the case together aren't twisted. If they look like they are twisted, simply loosen them slightly and twist the starter back to where the bolts are straight and re-tighten them. These starters also get very dirty inside and a good cleaning evyer few years will insure that you're getting the best service from it. The only true wear part of these starters are the brushes. The Yamaha part number on the brush assy is 5A8-81840-10-00. They run around $45.
Excellent Forum Thread With Pictures: http://forums.delphiforums.com/yamaha1100/messages?msg=52389.1 - Thanks Howard!
Also appears that an incorrect setting on the TPS is a major contributor to the dreaded clunk - either on starting or on engine shutdown. Included in the TPS section is an excellent article with pictures on how to check and adjust the TPS setting if needed. Click HERE to jump to the TPS section.