The door surrounds are Bestop? I have the same uppers and mine fit very well with a hard top and pretty good with Bestop surrounds.
Yes, I have the Bestop surrounds. Mine don't fit well at the top corner and the seal at the back bottom doesn't hit anything at all on the surround. That part isn't to much of an issue, I can easily put a piece of foam window seal on the back section that does go over the surround. It is the top rear corners that are the worst.
I feel if I had a new seal and could put it on the upper so it goes right along the outside edge instead of the inside, it may work a bit better. But it still seems like the whole upper could sit bit higher.
Here are the 2 problem areas. This pic here is the part I'm talking about at the bottom. You can see how the seal on the door doesn't even get close to the surround. This isn't a huge issue.
This is the main issue. Both top corners have gaps. The driver side isn't as bad, but still has a gap.
I do have to say that after driving to work and back, I really like them. Even stopped at a Starbucks, and even though the window doesn't open that much, I was still able to easily pay and get my drink. Now one isn't going to be bringing in a 4 cup cupholder from McDonalds, but it is still not bad as for as getting drinks.
It did rain a bit during the night when it was parked out in the parking lot and I didn't see or feel any wetness on the inside. Not sure how hard it rained though. I also drove it home in a sprinkle and I didn't get wet, so that is a bonus. LOL Not sure how my "fix" for the corners will do in a downpour but I guess I will eventually find out.