If you grasp the output flange on the transmission output shaft and turn it back and forth, do you feel like it is engaged/connected to the shaft?
If (hopefully) your gears are still intact, it might be that you lost a lobe/ear on the spring-loaded intermediate shaft inside the transmission. They don't often break, but if they do it could give alot of noise, somewhat disconnected feeling, yet not alot of metal shavings - provided that you stopped soon enough before things started to grind up. I've also seen one (Rare) case of the spring actually breaking - the owner was still somewhat able to move the bike on its own power, but it was not at all a smooth ride.
The part(s) I am thinking of are #5,6,&7 in this fiche-

....Errr, oops, sorry for the ridiculously small size... image copied from MAX's fiche library didn't work so well. You want to look up Diagram#23_0257 in the R65 parts fiche..
http://www.maxbmwmotorcycles.com/fiche/DiagramsMain.aspx?vid=51897&rnd=04302013I may very well be wrong on the diagnosis, but it kinda sounds similar to 1-2 threads I looked into a couple years back on another forum.
Fingers are crossed for you, but with so little oil in the gearbox, I assume that there was alot more friction than normal throughout its innards.