I have a 2003 Softail Standard EFI. It is about 500 miles from the 20,000 service. I have this weird vibe sometimes, it can only be felt at about 15 miles or less, you can notice it the most when at a stop. Some times it is accompanied with a knock. I have adjusted the clutch, all the fluids are good. When I put the bike on the stand, start it, put it in first with with clutch lever pulled in, the rear tire will start to spin. The knock feels like it is coming from the primary. Does anybody have any ideas on what is going on?
Rear tire spinning is not a problem. You have hydraulic drag of the fluid between the disks being spun by the drive disks and "pulling" the driven disks. With the tranny in gear, it will turn the rear wheel.
The knock and shudder or vibration is more disconcerting. I would open up the primary and check that the compensator nut is tight, and that the primary chain tensioner is in good shape. While you have the primary cover off, inspect the drive and driven sprockets to make sure all the teeth look OK.
Also inspect the drive belt to make sure all the teeth on the drive belt look good.
I think that bike should have the "B" engine. I am not experienced with all that mechanism in order to know what can go wrong with the balancers. Glider or one of the other guys here with hands on experience should weigh in on what to look for there.