knobbly

Well, i am here tearing my hair out and i am running out of time, i am hopeing someone out there can help me. I am due for an extended tour of Europe and Asia next week and my 97 XTZ660 3YF has is causing major concern. The weekend before last i was in Wales. Very wet day and very muddy. I went through a few deep puddles at not an excessive speed but shortly afterwards the bike cut out dead. No electrics at all with the ignition on. Anyway, i found the problem to be the main fuse had gone, but when i replaced it the bike would only start with the sidestand up and when i put it down once it was running it would try and cut out. Furthermore none of the electrics would work when the ignition was on unless the sidestand was up. Anyway, i removed the sidestand and this seemed to solve the problems with the electrics. ie. all worked ok when the ignition was on. I got the bike back together and it start fine, but as soon as i pop the bike into gear it tries to cut out. I have been through the wiring without finding an obvious problem and as i say i have two guys relying on me to go on the chunnel Easter weekend. I have been advised to cut the clutch switch and join the ends but am reluctant to go snipping more wires of unnecessarily. If anyone knows of the cause and a remidy i would be eternaly grateful. regards Knobbly