Hmmmm, interesting. It's not going to be clutch related, the clutch is before the transmission, a problem with it affects all gears, with the exception of slippage which generally affects the high gears first, but that's a silent problem. Considering you are *only* having issues in 3rd gear, that pulls the focus off of everything except the transmission itself.
Most likely your third gear set, either on the input or output shaft, maybe both, has had a couple teeth knocked off. Here's the big problem though, each time the gear moves through that area, it's going to free spin and then slam into the first good tooth, possibly cracking it or breaking off more teeth. Those teeth are now free-roaming metal in your crankcase.
They can get into and damage/destroy other gears, even crack your case!
I wouldn't ride it anymore, heck, I wouldn't even start it until you can split that case and figure out what's going on.
Check out this page.....
http://www.gadgetjq.com/transmission.htm
Scroll down to BMW 1150GS transmission. Obviously, you don't have a BMW transmission, but pretty much all motorcycle transmissions are extremely similar. I'll bet you that your third gear pair of gears is goobered. On that tranny, it would be the fourth pair of gears from the top.
Si