Just went through that exercise with my 67 BJ8. I found that the vent window was a little to far forward. I had already noticed the door glass wobbled a little when I rolled it up. I used a rubber mallet and tapped the vent frame back, that cured the door glass wobble and gave me the clearance I needed for the vent to windshield fit. I did have to open up the mount holes on the inside of vent frame with drimel tool.

BTW, the botton windsheild seal was one of the hardest pieces I have ever dealt with as well. One end kept coming out (after I wore it out pushing on it) I filled it up with gorrilla glue and clamped it. Not happy with how I did it but looks good.