As with most sounds and noises,finding them is usually a process of elimination.
When the engine gets warm and you hear the noise,stop the bike.With the engine still running,put it in neutral and safely hang your head down toward the clutch cover,while pulling the clutch lever in and out,listen for a change of the sound as the lever is moving in and out.If you get up close to a concrete wall,the sound will be easier to hear.
If the sound changes back and forth when moving the lever,the outer tangs,and or the inner teeth on the clutch plates are most likely rattling in the basket and hub.
Some noise in this area is normal and is usually contributed to hard take offs like drag racing,or having fun when the traffic light turns green.
If the noise is in the clutch,find another V-Rod owner w close to as many miles on as yours and do a comparison.
My 03 clutch made excessive noise in the clutch and I installed the SE basket and hub.It still makes some noise when hot,but I consider it normal.
If the basket gets grooves in it that are not acceptable,you will notice erratic engagement and possible binding when shifting into 1st from neutral,because the outside tangs will get stuck in the grooves.This means time for an inspection and replacement of the worn and damaged parts.
If the wear is excessive,an oil analysis should be able to find unacceptable amounts of aluminum floating around.
Back lash at the clutch hub ring gear could cause a similar noise,but I havn't seen or heard of this problem on the stock V-Rods yet.