If the zx6r electrical system is anything like the zx12r one, which it seems to be given your problems, then it can still be a recurring problem - nothing that you've done wrong.
I have posted a fair bit on my fixes for the zx12r (with lots of advice and help from smarter people here!), and from a bike electrician here in Sth Aust.
Main problem - and this doesn't happen to all 12's - is that the heat/electrical energy generated by the Alt/Stator system overloads the stator wiring causing that to cook. Then there is either an oil wicking to the stator/reg connector or just heat melting or both to the connector. The bike electrician said the Alt puts out too much juice, and when the bike is stopped after a ride, say at a cafe, then there is no more oil cooling of the stator, then acts as a heat sink causing the stator wiring to cook and so on. His fix is to re-wire the stator with a LOWER gauge wire so as not to take on so much juice from Alt. Also I had a Japanese MOSFET reg/rec installed and different connectors etc.
Electrician said this is not a permanent fix but may delay the same happening again - and in my case it did couple of years later - but he fixed the stator again under warranty!
Others here have not had the same level of problems and seem to get away with just re-doing the stator/reg connector.