So I just paid off my used 2006 GS500 with a little over 5000 miles, and of course, that would be when I am having problems. I went to start it up about a month ago and it wouldn't start and made a clicking/knocking noise. My grandpa deduced it to being spark plugs. So we replaced the plugs. In the process we found the crumbling fuel line, and replaced that as well. We wanted to replace the spark wire as well, but were told that it cannot be replaced by itself, so it was replaced with a car spark wire (compression wire). Now the bike starts, but if it is doing anything under 4000 RPM, it sounds very throaty and continually sounds like it is backfiring. And before anyone suggests it, yes there is gas in there. :) Any help would be greatly appreciated.
Have you tried examing the spark plugs again after you got it to start up?
The condition of the spark plugs may be able to tell you more now....