Along with the oil change.....use a mineral oil...as opposed to one with synthetic additives as these may promote clutch slippage.
Idle speed should be around 1100 rpm.
http://www.datateck.com.au/Lube/PenriteAus/ Start with carrying out the clutch plate and clutch cable adjustments as per service manual.
Physically disconnect the clutch cable from both ends and check there is no binding and it slides freely in the outer sheath..........any snagging or stiffness in it s ability to move..............replace the cable.
It would actually be something worthwhile for the price of one just to eliminate it as it may catch friction under tension /
operation. You would probably see this at the return of the lever on changing. There should be a half inch or so freeplay at the end of the lever before you feel clutch pressure.
I m assuming you have changed the oil and filter from when it has been sitting for so long. I may even suggest after a couple of reasonable rides..........you change it again to really flush out any old oil residue.
These bikes do have a tendancy to "clunk" into first gear from time to time........especially on first start up .
The fact that you say it occurs in other gears sounds like it s clutch related.
The main thing to find out..........is it gearbox/clutch related.............or is it a ...........drive train / back wheel isssue....or other.
Raising the rear wheel off the ground and rotating/pulling on it in different directions with it in gear as well as in neutral to see if there is anything abnormal .
With the bike in gear and the rear wheel off the ground..............have someone pull the clutch in ....or use a cable tie to hold it.......... then rotate the rear wheel to check the clutch has released.
Try this when the bike/engine is cold ......................as well as after a short run to warm things up......to compare.
The gear shift selector may also need inspection.......but start with adjustments /oil changes .....then try to narrow down where the problem may actually be after that.
One other point to note is you say it is rev related............carrying out synchchonising and the colortune operation on the carbs has a direct effect on how the engine/revs and the rate at which the engine settles down inbetween gear changes.
For example..........out of tune carbs...........don t allow the engine to go back to idle with the revs tending to hang ....on changing gears .....
once adjusted properly.... a quick blip on the throttle should see no lag.........or hanging on revs.....the engine should settle quite quickly.
Gear shift lever linkages should be adjusted and checked as well.
Hope this helps.
Jeff