roof rail weatherstrip isnt fitting well

I'm sorry for you.. been there done that, wish I had kept both old seals.
I've got the ones from steele rubber and they are the best fitting, not like the originals but at least they seal.
See this post for all of the heartache...
http://www.forabodiesonly.com/mopar/showthread.php?t=50949

..oh, and I did have to do the whole "window adjustment" thing... like 2hrs per side, and wasn't ever able to get the passenger side quite right...