From KTL Restorations; Our cure for installing this less than perfect fitting reproduction is to use the longer trim clips (black ones). The clips Ford used were red oxide and the reproduction clips are green. The black clips extend up about 3/32 of an inch further, this should be enough to grab the trim. Also, not all of the clip posts were in the same location as far as some being higher or lower which would puts the clip closer to the pinch-weld or near the body line. Sometimes he has to use a combination of clips is needed to complete the job. You have to be careful not to get the clips too high or the trim will be loose.
From Cascade Classics; My trick is I put the seal on the body of the car first and then work the glass in. It is a pain in the a%# but it works. The clips I use are #387. Ford part number D1AB-6545413-AB or C5ZZ-6542413-B. I have never had a problem with them.
From Jeff B, President on the Cascade Cougar Club; I use a dremel tool to bring the height of the rubber seal down as the only reproduction made (by DCMR) sits up a little too high.