A couple more things to look for:
To see if the vacuum side is working properly, turn the adjuster ring on the top of the Scottoiler to the fully anti-clockwise position - this is the 'Prime' setting. Get the bike in a safe position where you can start it and see the piston in the Scottoiler at the same time. The piston should rise by about half a cm when you start the bike, and stay lifted. If this doesn't happen, you've probably got a lose pipe between the scottoiler and the carbs. Your bike may well be backfiring on the overrun as well because of the air leak.
If the piston is rising, and you have recently run out of oil, you've probably got an airlock in the oil delivery pipe. With the system still set to 'Prime', look for the little black filler pipe on the side of the Scottoiler that is used for filling. Plug the oil bottle into the filler pipe and hold the bottom of the filler in place. Now, hold the oil bottle upside down and squeeze it to force oil through the system. This will blow any air bubbles through and hopefully everything should be fine now. You should put something under the oil nozzle because you will inevitably blow some oil out at the same time.
On the 'Prime' setting, you shouldn't need the engine running to blow out the air bubbles.
If this doesn't work, I'd look for kinked or twisted pipes.
There is some F650GS info here
http://faq.f650.com/FAQs/ScottoilerClassicFAQ.htm
And general fitting photos at
http://www.scottoiler.com/support_guide2.asp
HTH
Tobes
