Rain Troubles

Hi,
I own an LML Freedom 110 CC bike.
I 'm encountering a few problems when riding in the rain.

The engine gies OFF and then comes back ON(due to the forward velocity).
If I'm going up an incline, the engine won't come back ON. I'd have to wait out the rain.
Immediately after the rain, the bike would function perfectly.

There is nothing wrong with the spark plug. I have given it a waterproof covering. but still the problem persists.

I've got some problem with the clutch. The mechanics said it's because water crept into the clutch cable sheath.
Could that be a reason? could water in the clutch cable switch off the engine? (Forgive me if this is a crazy question )

I'm not much of a bike mechanic.
so, all those techies out there, please help me.
All u need to do is point out at what all places in the bike can the presence of water turn off the engine.