Riding in rain ,How to protect wires/electrical components?

Make sure the magneto cover is sealed good. If the gasket is dry rub some 2 stroke oil on it or use silicone rtv gasket maker. Where the wires come out of the case put some silicone there as well. As for the cdi it should be fine as long as is not in direct hard spray from the tires. If the magneto gets wet it seems to kill cdi boxes in my experience.
 
Like Spare Parts is suggesting, the place on the engine where the wires exit, there's a black rubber grommet they usually pass through.

I'd get some Silicone window sealer and smear a little around the grommet opening in the left engine casing and inside the grommet where the wires pass through. Leave the magneto cover off while the silicone gel cures, it off gasses Acetic acid for about 48 hours and it will corrode parts.

Silicone the thin gasket to the magneto's cover with a very thin smear of silicone gel. That should seal up the magneto. After testing to see if all of the electrics all work well,( coil and kill switch..) I would also cut away the push on connectors for the coil and kill switch and directly solder them to the wires of the engine, so they are sealed together with heat shrink tubing to keep out the dirt.

I'm recommend fenders for bikes because the rain you will eventually encounter will spray water and road dirt everywhere on your bike. A front fender keep the worst of the dirt off your pedal chain and the front of your engine where the wires exit, the rear fender keep you clean and dry
 
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2 stroke 66 cc

Can I make a suggestion?

Consider the 48 cc engine if you can get it, as a general rule the 48 cc bicycle engines run smoother than the 66cc's, they don't make as much power, but it will create less trouble down the road as far as loosening of fasteners and breaking stuff from vibration fatigue. Don't forget to use some sort of blue colored thread locker on any critical fasteners on your bike, even the 48's buzz a bit and that will loosen parts.
 
Poor guy probably just bought the engine and you are telling him to buy the weaker one, oof.
 
Poor guy probably just bought the engine and you are telling him to buy the weaker one, oof.
He's wanting to use it to take a long trip on. I've ridden a couple 66 cc engined bikes they vibrate pretty intensely. My own 48 isn't super smooth, but, it's much better at 27 mph than the 66's were at 19 mph.

So yeah if you had read my entire post you would a noticed why I suggested this, vibration kills bicycle components. There's no indication he's already bought this engine yet and he's free to ignore me.
 
I've built and worked on 100's of bikes 48, 50, 60, 66, 69. Their are good ones and bad ones in all sizes. A few random comparisons is a bad idea to make general assumptions for anything. To each his own, but I could not disagree with you more on choosing a 48 over a 66. Especially for a long trip with extra load.
 
Back to the topic,
I omitted the kill switch entirely to protect it from rain. :)

I also soldered the two wires from the magneto to the two from the CDI, rather than use the spade connectors.
I cut the mag wires short to put the solder join inside the mag cover.
I made a drip loop in the CDI wire so any water on the wires will drip away from the rubber grommet.
I used silicone sealant just as others have said.
I left a tiny gap in the very bottom of the mag cover gasket to allow it to breath and expel any condensation moisture.
I covered the upper part of the mag cover gasket with pvc tape. Just in case.
I also added a rubber shroud to the spark plug wire where it enters the CDI, just like the one at the boot (it actually was the one from the stock boot) and just taped it in place.
I used an NGK boot and plug.

And fitted the bike with fenders. :)
 
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