The problem doesn't necessarily have to be with cylinder 6; it could have a completely different cause. I once had a BMW where the catalytic converter was clogged, and it only ever misfired on cylinder 2. I tried everything and replaced parts until I finally replaced the catalytic converter, and that solved the problem.
Your problem, of course, isn't due to a clogged catalytic converter; that can't happen in the rain.
But it could be, for example, that a lambda sensor cable is the problem. When it gets wet, the engine receives incorrect lambda sensor readings, leading to poor combustion, which in your case is causing problems on cylinder 6.
In any case, water in the rain is more of a problem at the front of the engine and underneath. Very little rain reaches the top of the engine or control unit.
I would put the car on a lift and inspect the cables from underneath.