Running

[Bob]

It still works in my 17-year old KTM, and may well have saved me several explorations of the carbs in my old ZZR600 during the years I was commuting on it.

[Farad]

I have the same bike and have also had rough running issues. Eventually I bit the bullet and rebuilt the carbs (twice, second time to re-check the float levels as it was still not running smoothly). When I opened the carbs up they weren't as bad as I'd suspected, especially after running E10 and also regularly leaving it for several weeks at a time (fair weather rider only). The O rings and rubbers were replaced as a matter of course but they didn't look too bad and I now wonder if the E10 issue is a bit over hyped. Having said that, although a bugger to get out, the carbs are dead simple to rebuild so it may be worth doing.
I took it for a long blast this Sunday (thanks again Brian) and it performed very well apart from an intermittent power drop.
I've concluded that there was probably an underlying electrical issue all along and will now start looking at the HT circuit.
Not sure that this is in any way related to your issue but as you've been changing plugs I'd certainly double check the HT leads and the low tension connections on the coils in case you dislodged one.
Do let us know if you get it sorted.