You're just talking the slop between the gear engagement dogs. That's normal. the slop goes away when you engage the clutch because of clutch drag and the pressure the clutch release mechanism has. all normal.
Now I have to make the assumption that your chain isn't new because I haven't seen anything in the previous about replacing the thing. The stock chain is just about as bad as the Skidmasters. But just getting back from your long ride, I'm guessing your chain is totally shot. A worn out chain will cause vibration by itself because of all the flexing it can do which also tears up sprockets. Have you changed it since you got back? How many miles does have on it ? The way your talking about it now sounds like it's just totally shot with the instant readjustments and such. You can't properly adjust a worn out chain. There are too may points of slop to be taken care of, even if it's a new chain it's sounds like a bad one.
Just don't replace it with an OEM chain. Two things that should be taken off a new RE are the stock chain and the Skidmasters before they roll out the door. I know I'm gonna get blasted for this, but I know the Skidmasters still suck, I hear rumors that the chains are better, I certainly haven't seen any proof of that. Mine was totally shot in 6500 miles, but hadn't started eating up the sprockets. When it got down to needing to be adjusted ever 200 miles, it wasn't going to be long before the sprockets would have gone away, too.
The chain wear limits are: Pulling the chain up off the rear sprocket, 5MM, about half the tooth height. Max Chain length across 21 pins, 328 mm.
Bare