Go to the R65 Wiki section of this forum, under Repair->Transmission->Clutch Replacement and that should give you all the info you need to remove the gearbox, without having to move the engine - or completely removing the swingarm (which you've already done anyhow..
A couple bolts in the front of the airbox bolt through into the rear of the engine casing, so it's gotta come off (see pictures). Also, DO NOT MESS WITH THE SMALL PHILIPS HEAD SCREW THAT YOU WILL SEE IN THE TOP/MIDDLE of the gearbox (revealed when airbox is removed). It is holding a metal plate inside the transmission, and if you remove the screw, the plate can become dislodged, and requires a complete dismantle of the gearbox to refit it (very $$ if you otherwise don't have to crack open the gearbox).
Best of luck with the investigation. IT may be that the output shaft bearing is going, which would be a not-too costly repair. There is however, an internal shaft with lobes (like a similar version of what itoward the back end of the drive shaft in the swingarm. It isn't very common, but not unheard of, for one of the lobes/ears on the mated internal shaft to break. I am hoping that this isn't the case with yours, but it is starting to sound a little familiar to a another case that I have heard about. Fingers are crossed for you..