Clutch niose?

Probably the mainshaft nut has come loose. Whip off the clutch spring and tighten. Or maybe it's the crankshaft nut. Is the primary chain adjusted and aligned correctly with gearbox studs fully tight?

When the clutch is engaged the release bearing isn't doing anything so unlikely to be that. If the mainshaft nut is loose the clutch can rattle around one the splines. If the crank nut is loose the alternator can rattle around and maybe kiss the stator.

If possible run with the case off .No harm done short term.

Sounds like a main bearing is shot, don't ask me how I know, ask my opposite number. His bearing had bad pitting across a tide line where the bike had been left standing and the nasty stuff sat on top of the oil and attacked the bearing. 

No, any attempt to disassemble the clutch without the tool is life threatening.

you can take the adjuster nut off, but pretty sure hole is way too small for access. Tool is not expensive, and IS needed for more dismantling.

Perhaps the circlip behind the clutch has popped off and the basket is catching/rubbing the inner chain case?

That circlip behind the clutch has failed for me in the past. Probably re-used too many times :). But the mainshaft nut coming loose is common enough with just the locking tab used, again often re-used too many times, or just the spring washer on the earlier bikes. Worth putting some loctite on the mainshaft threads.

And, if you can't eliminate the noise you should check out Ashley's suggestion about the mains. Using a long socket extension bar placed to your ear, touch the other end to the gearbox and crankcases to narow down the location of the noise. Probably best to put the primary cover on while you do this. A stethoscope is even better if you can lay your hands on one.