Gary, 

do a search for POR patch, it's a caulk type POR product for just this purpose.. 
sure it's not bodywork 100% perfect weld in rust repair..  

but it's probably worth a try.. 

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Date:    Thu, 1 Feb 2007 14:23:21 -0800
From:    Gary Bawden <goldfieldgary@YAHOO.COM>
Subject: Re: Removing window seals

Hi again,

OK, got the window out! Thanks everyone for the help. Now for the bad news! The rust spot is worse than it looks - - light tapping with the pointy hammer has revealed that it is rusted all the way through in two spots along the 6" rusty bit along the bottom. Now what - - according to my 1959 edition of high school body work book gleaned at a yard sale (complete with pictures of shop guys with flat-top haircuts), I should get out the torch and weld in new metal. Or will epoxy and/or fiberglass be the more modern, preferred approach? I have a deep-grained mistrust of Bondo-type stuff, but I don't really want to make this too complicated.

Gary