Nice bike. Is it in as good a shape as the photos? If so, I hope you don't do a cafe conversion.
First thing, the filler cap is backwards and will let rain in the tank. There is a drain hole that is covered when the cap is like that.
As far as the noise, I am thinking Universal joint at the front of the drive shaft. If it was mine, I'd start with making sure the engine is good, and then pull the transmission, and swing arm. Do a complete spline inspection and lube, including the clutch splines. You will also want to do the o-ring on the clutch while you're in there as well.
The good news is that the transmissions are clunky, but fairly bulletproof and the drive shafts and final drives are fairly common and reasonable priced on eBay. There is also a shop in Canada who can rebuild the driveshaft and final drive, but I hear he isn't taking any new business right now. I have heard there is another rebuilder, but I can't recall who or where. Maybe someone else can chime in with their information.
Good luck, looks like you have a nice project there. Keep us posted on your progress.