I could be wrong (wouldn't be the first time), but I don't think the Dyna jiffy stand has a bumper actually attached to it like the Touring models. It's on the frame, and the stand just rests against it when it's in the "up" position. Have someone hold the bike upright, fold the stand up, and look for contact between it and the frame. If there is no rubber bumper still on the frame rail, you can fabricate something out of a piece of garden hose or something similar and glue it in place until you get to the dealer for the correct part. If I remember correctly, I made my own on my '99 Dyna after the original fell off and it was still working just fine several years later when I sold the bike. Sorry, but I couldn't find any pictures or drawings.
Jerry
Edit: OK, I was actually right and my memory isn't totally shot yet. I'm attaching a pic of the frame mounted bumper that snaps over the frame rail. If it's missing, that is what's causing your noise and vibration.