In November my Mach 1 will be 2 years old. It's a daily driver ran or shine. I've never had any problems driving in the rain at all, even in some serious downpours at freeway speeds.
never had any problems with my mach 1 only had it for sixs months but its my daily driver to. you might want to check your run off points for your shacker. the mach1 has a main run off in the front left hand side that runs strate down check to see if you can repeat this system with yours maybe
There is actually 3 drains on the Mach 1 setup. If your really having problems in the rain I'd make sure that the housing that holds the airfilter has the "weep" hole drilled into the bottom of it