I have read many posts about this problem. My experience is this. I would hear it randomly on shut down on a 1998 1200 Sportster for ten years, and never had a problem. I now ride a 2012 Roadglide Ultra with 35K miles, and it randomly makes a clunk on shut down as well. However, I have noticed with my Roadglide, if I shut it down with the bike in Neutral, -NO CLUNK! -Go figure? I have also noticed no "Hard Starts" as well. This is just my observation from my experience. Maybe try shutting the bike down in Neutral?
2012Road GlideUltra-Vivid Black,Vance & Hines Two into One Pro Pipe,Screamin' Eagle Race Pro Tuner,Screamin' Eagle High Flow Air Filter,16" L.A. Choppers Apes,16" Klock Werks Windshield,Hogtunes Big Ultra RG Audio Upgrade Kit,"Tall Boy" Seat,Chrome Levers,Grips,TurnSignalVisors. Powdercoated Fork Lowers&Cowbells,Metzeler Marathon 888's,Gold Valve Cartridge Emulators,GloveCompartment, Saddlebag,Trunk and Lower Fairing Liners,Highway pegs, Legend Revo-A's,Hog Trough Cup Holders