As others have said, the reason it clunks so loudly is because it is a wet plate clutch and after sitting overnight the oily clutch plates tend to stick to the transmission drive plates.
Once broken loose, everything returns to normal.
The next time you want to start your RE do the following:
1. With the key off, shift the transmission into a gear. Any gear will do.
2. Flip out the kickstarter lever (assuming it has one**).
3. Pull in the clutch lever all the way in.
4. Using the kick lever, with the clutch still pulled in, kick it thru several cycles.
5. Move the transmission back into neutral and release the clutch lever.
6. Start the engine, pull in the clutch and shift into gear. It shouldn't klunk any more than it normally does when your riding it.
I think doing this will break loose the sticky clutch plates before the engine is started.
Then again, I have been known to be wrong before.
** If the bike doesn't have a kick starter the only other way to break loose the sticky clutch plates is to put it into gear, pull in the clutch and use the electric starter.