My2 cents! The rectifier and CDI are basically waterproof so they don't need any extra protect other than die-electric grease on all connection as Tom suggested and mounted in the air flow as they both stated. The blade or bullet type connectors need additional protection- a simple protection method is shrink tube, you can slide this over the plugs, connect them and center the shrink tube over the joint and heat it up, it'll still be accessible and sealed. Mounting everything in a box is for organization purposes only, I mount electrical components on the horizontal bar behind the seats- I'd hope you never go that deep!!! it's very easy to access.
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