Jim,
I had this thread forwarded to me and I wanted to give you some feedback. Looking at this engine I would date it to be about 6 or 7 years old. The starter brace is missing and that was added in 2005. The ignition is not the PVL system that was implimented in 2006 and so on. Not knowing the history of the engine we have no idea how many hours are on it. I'm guessing more than you think.
The clutch also is a likely factor for why your sidecover bolt torque was an issue. Right down to the gasket material these engines are engineered to dampen the majority of the harmful harmonics that come with racing. Even with that the repeatative engaging of the clutch or slipping of the clutch over time all loads up through the side cover. I would recommend rebuilding your clutch and even look at lower engagement springs. This will allow the clutch to function properly and limit the in and out pounding. Ultimately I would recommend checking your sidecover and head bolts on a regular basis just as part of your normal engine routine. These are engineered for racing but the harmonics, a lean condition, or just the pounding over time that comes from racing mean we need to have a general engine routine. Everything from the track surface to an out of balance tire feeds right back through your hard mounted engine.