The bike will start and rev real high in neutral but when in gear run fairly normal until the clutch is pulled in then will rev to the moon either hot or cold?
SOURCE: 1991 CR 500 (reving to high on idle high serges)
take some wd 40 & spray around the carb boot while running to see if the idle drops for a few seconds. sounds like you have an intake side air leak causing a lean condition making the motor rev high.
SOURCE: my honda vf 400 f is idlind very high and than
well the idle drops because the clutch is slipping making the engine work harder at idle so adjust the clutch on the lever and to drop the idle on carbs there will be a screw this is the idle screw turn this out until it idles at 1000rpm buddy get back to me if no difference 
SOURCE: High pitched whining noise which doesn't vary
My bet is that it is actually coming from the speedometer. Try disconnecting either end of the speedo cable and see if the noise stops. If so, then all you need to do is apply a drop or two (but no more!) of oil into the speedometer-head bushing. Do this by removing the instrument cluster so you can flip it over - then put some light viscosity oil into the area where the speedo cable goes in. CAUTION; do not use more than one or two drops of oil - and do not leave the instruments upside down for any length of time. Failure to heed these warnings can cause oil to drip onto the face of the unit, making an unsightly (and un-fixable) mess.
Please let me know if this fixes the noise.
Testimonial: "Thanks very much. Problem solved - It used to whine like a banshee now it's sweet. Three cheers to you. You are the man ! Davydd"
SOURCE: VFR400 NC30 - Idle and gear problems
tHE CLUNK YOU TALK ABOUT WILL BE BECAUSE THE REVS ARE TOO HIGH, AS FOR THE HIGH REV'S, COULD BE SOMETHING TO DO WITH THE OTHER GUY HAS NOT ADJUSTED THE THROTTLE MECHANISM PROPERLY
SOURCE: I have a real hard time getting the bike started. ...
Many of those CRF have problems with the valves, check the valve clearances, as well as all the general maintenance items, clean carb, clean air filter, new plug.
If the clearances need more than one number smaller on the shims, it may be the start of valve regression.
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