i had exactly the same problem on a 99 Sv650. the offending part was a split carb to cylinder head rubber. $90cdn later and it's running like a top again
Just a silly point, but there isn't an ignition cut-out on the injected SS, is there? Clutch interlock? Sidestand interlock?
I've had this problem on other bikes, and it was the result of the bike, at certain revs, hitting exactly the right vibration frequency to cause an intermittent fault. And then, of course, it got worse and worse.
It's much easier with the fairing off and tank propped up. I changed my plugs today and cleaned aforementioned contacts; there's still a glitch around 3000...
Mother Outlaw is staying with us at the mo, seeing as her daughter was due to give birth today!!