First on topic: With the engine running spray some carb cleaner around the base of the carb and check for a vacuum leak. Next check for the distributor to see if it's horrible worn and that everything is grounded. Carb and ignition problems give the same symptoms. To me it almost sounds like distributor bounce but it also has the symptoms of a vacuum leak.

Now off topic: NSR500 as a long time owner of over pumped RD's and having road raced Honda 125 GP bikes it's really hard to beat the joy of a screaming 2 stroke..............the 1200 is fun in the ride the Poo out of an old CR80 way but never going to be the "oh my God this thing is gonna kill me of TZ/RD/RS/ NSR or ported CR500 thrill"

Tom