Be careful with those "Works now and I don't know why" solutions. They could strand you who knows where. Like Red01 said, it doesn't make sense to have 3&4 go out when they're on different coil circuits. That would at least point to the carbs. Something to think about - have the carbs ever been removed and cleaned, tank drained of sediment, etc...
That said, my 12er ran like crap once, back in 2000??? after checking the valves. I found that it was arching to the case and that the ignition wires had to be kept as high as possible in those bendable routing clamps that Suzuki supplies. Solved.
Take another look and rule out the obvious. Nothing worse than not being sure you can make it home once you leave the garage. After all, it's not a Harley (ouch).
Marc/Atlanta