Yep, those are window channels and they continue into the door, hard to lube them down there but if you apply enough lube to the portions in the actual window frame, that helps. I know the spray lube gets on the glass but it's simply removed with some decent glass cleaner. The scraper you speak of does cause some problems because it dries out fairly quickly due to its location. You can treat it just like a misbehaving wiper blade and liven up the rubber with a coat of household ammonia. I also had some luck with that Rain-X stuff but it doesn't last.
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Roy Olson