ssim, sorry I wasn't clear. I'm only concerned about the inners of the body from the dusty ballgame and non-sealed lens (28-105) and outer elements of the 17-40 used at the beach.
At the beach, with the 17-40, I thought there were dust spots on the lens, I knew it wasn't sand, so I took my bulb duster and attempted to blow it off. When it wouldn't come off I used my pen duster and that's when I realized that it was fine water spots, not dust, which I ended up smearing instead and are still there. So I thought a cleaning would fix this.
Yesterday, at the dusty ballgame, with an older, non-sealed lens mounted, everything just quit. It gave an error message about the lens not communicating with the body and something about the contacts. I figured that dust got in and could be causing the error. It hasn't happened again, but wouldn't want it to at an important event. So I figured a cleaning may also fix this.
In the old days I would have simply used lens cleaner for the lens and cleaned the contacts with distilled water and a electronics based cotton swap. But again, since my warranty is still in effect why screw with it. And on the other hand I'm not sure I'd use a liquid based cleaner on optics any longer. What's the norm today for cleaning a smear?
Lowner, The reason they covered the cleaning the first time around was that the body was having AF problems and that was included with the repair. Since I got an error message about communication between the lens and camera I thought the same would apply for the body. The lens I thought couldn't hurt to ask.