R100 ignition problem

Got my '83 r100 winter project mot'd recently and got it out for my first proper run on it since I bought it late last year. The bike has done 87000 miles, only 60 of which are mine!

Set out in nice weather got about 30 miles into a 60 mile journey when the heavens opened and never stopped. I got within 3 miles of home, at the end of a dual carriageway, when the bike died, suddenly, without warning. I have extensively rewired the bike, moving the main terminal board and relays under the seat to allow an xt500 headlight to go on. As there was no coughing and spluttering involved, no running on one cylinder, I considered that the high tension side was not the cause. I suspected it was a dodgy connection on the low tension side and held my rewire responsible. Before I even had chance to get the tank off, a passing kind person in a van rescued me and the bike.

I spent 2 nights trying to find the faulty connection, to no avail. I started to suspect the ignition trigger unit. Removing the front engine cover I eventually realised there is a 3 pin connector block, connecting the trigger unit to the ignition control unit. The connector is half hidden behind the diode board. This connector block has hollow spaces inside and had filled with water. 

Drying it out cured the problem. 

How did water get in there?

 The front engine cover, although vented, is actually quite a water tight design, except for where the wiring looms pass through it at the top, under the tank. One of the rubber blocks, through which the loom passes, was not located properly and had dropped down (not my handy work, but I should have been more diligent). This had allowed water to run down the loom and fill the connector block, which hangs vertically. These two aspects are the weak points in an otherwise sound design. 

When the bike is off the road this winter I'll re wire that bit to include a "U" in the loom before it encounters the connector block. That way any water which happens to run down the loom will drip off before it can enter the connector block. 

Anyone recommend any silicone based product to fill the connector block, but still allow the thing to function?

Another thing I learned along the way, which doesn't seem to be mentioned in the Haynes manual, is that the ignition seems to be a "wasted spark" system, even though 2 coils are used. This is very relevant to understanding the circuit and hence thinking through any problems.

Hopefully this little story might just benefit someone else at some point.

Any other handy tips gratefully received.