Last time I drove in the rain, my entire back was one long strip of mud. From my helmet, to my neck, etc.. I expect to get dirty when driving a bike like this but it was a little excessive. I finally decided to add a rear fender to the back side of the bike. I haven't tested it to see if it captures the break away water or not but I am sure I'll find out shortly! I had to screw it into the rack as the real estate on my seat post is a premium, due to my short legs!
As for the controller I moved it from the bag to a custom center tube device that give it plenty of breath and out of my way. It's a simple pray painted electrical elbow that I cut the guts out of with a steel saw, sanded and painted flat black. I put on new pedals too as the last ones cause my feet to slip off when they got wet.