The tubes are supposed to run all the way down so that the bottom of the tube is spitting water out at the rocker panel just behind the fender/door seam. The rear tubes are supposed to run all the way down to the rocker panel just in front of the rear wheel well. I would try and run your wire snake down each tube to see if you can figure out where they are routed. It sounds like the tubes have shrunk/become brittle and broken, or have not been installed correctly from the factory, or over the years they have become dislodged or moved. This poor drainage has been the reason for a lot of rust problems with sunroof cars.
Scott.