[chrisw]

I've just had similar problems on my 999. Misfires, uneven idling, revs surging and loss of power. All occuring after heavy rain. I have now traced the problem to the ignition lead connector to the coil pack on the vertical cylinder. The waterproofing gland on the connector had split (infact there was a big chunk missing). This was letting water into the connector. A liberal spray of contact cleaner and wrapping the connector with self-amalgamating tape seems to have fixed the problem. New superseal connector on order for a proper fix.