Do you have the finned head bolt cover bridge? If so remove them and check the mount cap that is on top of the head bolts. The allen set screw may have worked loose and may be causing the bridge to rattle at certain engine speeds. Had them work loose on my 05 SEEG and drove me nuts until I found one of them loose.
I had the same thing happen on my '06 SEUC with the finned bridges.
BUT, I also had a loose compensator nut on the same bike, another instance. It made a hell of a noise, but not all the time. However, you could feel it in the left floorboard when it did it. If it's the compensator nut, HAVE IT CHECKED IMMEDIATELY. I was fortunate that it happened in my home town and not on the road. Took it in, had the dealer properly torque the nut with red locktite and never had the issue again. I had to sell the bike when it had 25K on the clock, but once properly torqued, the comp nut will stay put.
One other mystery noise I had on the '06...when new, I had the automatic chain tensioner installed. All was fine. Was about to leave on a trip, and didn't have time to service the bike myself, so let the dealer do the service. During the trip, the bike started making a hell of a racket on the primary side. It would come and go, depending on speed/rpm and what gear I was in. On closer inspection, I could see fingerprints on the primary chain adjustment cover, which should not have been removed because the auto adjuster eliminates the need for manual adjustment. When I got back home, I determined that the brilliant HD "tech" had "adjusted" my auto adjuster, causing the chain to make an awful noise. I pulled the primary off myself, reset the auto adjuster...problem solved.