Aye stee,
This may be of use!
Link to manual download:
SLR650_manualAlso:
Exploded_diagrams_pricesWemoto, David Silver or your local friendly Honda dealer should have fiches and parts still for this beastie.
Check oil and filter for bits of steel, with a magnet. if you have been 'plonking' the motor, you may have stripped teeth on the gearbox pinions, hence the knocking noises as the gears spin and don't engage with missing or chipped teeth.
Check that the alternator (generator) nut is not slack and the rotor is not slopping about on the taper with the woodruff key alone preventing it spinning. The woodruff key will let go and the taper will resemble the rough side of the moon!

Check that the balancer weight and its drive are all secure. Check timing of balancer weight.
Check that the clutch centre nut and the nut retaining the primary drive gear on the end of the crankshaft, are all tight and tourqued to the correct value. Any slack here could result in catastrophic failure of the primary drive.
Whatever may be the trouble, STOP RUNNING THE MOTOR UNTIL YOU FIND THE FAULT!!!!!! If it locks up whilst you are riding it, it could be curtains!

Sorry not to be more specific, but only you can hear the knocking.
I hope this helps. My regards, Bill.