The XR650R is a fairly smooth running motor but is known to have a variety of rattles and ticks. If your motor seems to be making a little extra noise lately the cause could be one of the below:

notes from JM-2008

Worn Cam Chain

Historically larger XR,s (old 350’s/400/500/600/650) use a ‘Morse Hy-Vo’ type cam chain.
Looks like a series of gear teeth as opposed to a conventional roller chain.
When new and in good condition they run very quiet.
As the chain wears noise emanates from the rear of the cylinder near the cam chain tensioner.
Usual sign of a worn chain is the noise will diminish as engine rev’s increase.
Strange as this may seem it is due to the chain riding up on the gear type sprockets and taking up the slack.
Suggest checking your chain is not worn and tensioner is not stuck.

WEAK CLUTCH BASKET DAMPENER SPRINGS

(at rear of clutch basket) - If these have sagged or lost tension the clutch will be noisy at idle and low revs, the noise will usually diminish when you pull in the clutch.

BALANCER

Have not had one out of an XRR but suspect it’s the same as with all previous XR variants. These traditionally have a ’spring loaded split gear drive’ to dampen drive line lash and subsequently noise when not under load.
One of the gears will be spring loaded and appear not to line up with the adjacent gear when not installed.
Should this item lose spring tension the resultant noise will be caused by clearance/back lash in the drive gears.

AUTO DECOMP CAM

(item #7 on the camshaft – http://www.honda-xr650r.com/honda-xr650r-cam-shaft-rocker-arms-and-valve-assembly-parts-fiche/)
Not much to do with this other than remove it.

Unless the clutch hub is notched from wear I wouldn’t bother replacing it, same applies to the balancer & decomp cam, very little to be gained throwing wads of money at the motor to find it’s still noisy!