I'm not sure if they're designed the same, but i know on the 3rd gen 4runners they have sunroof drainage tubes for the rear of the sunroof that run behind the passenger door and drain down behind the rear wheel. You might have a leak or clog in a sunroof drain line somewhere. when sunroof drains...
I have a 97 limited and the flares don't really bother me in size, but mine are kind of faded. I am considering wrapping mine in black vinyl or painting them along with my chrome bumpers.