I've had luck stopping leaking windows in some of my cars using a good grade of silicone caulk.  With careful cleaning before applying, and some planning on how you are going to get it into each curve and corner, you can simply retro-caulk around your glass and the body with silicone, then wash off the excess with a damp rag.
  The drill is to use a warm acetic acid (I use cheap white vinegar) in a warm water solution.  I like a soft cotton cloth, damp  and I rinse it off very often. Try to not get lots of water into where you've put the caulk.   Depending on the amount of mess you make applying the caulk, you may have to change the solution a few times before you get all the "Over-Goo" off your glass and paint..It seems to work just fine for me.  
  You may want to pre-wash all the rubber you can get to if it is at all chalky or oxidized.  I use a hardwood (or plastic) wedge to push the rubber away from the body and the glass..You can first time around chase your stick with compressed air to remove any grit that might scratch the paint or cause a window fracture...
  It is worth a try anyhow..
  Don Hanson