You will have to adjust the window to change those gaps. I just finished this project a few weeks ago. I do have some tips...
1.) Make sure the door hinge pins and bushings are not worn out, and the door is adjusted properly. Are you door gaps all the way around consistent?
2.) The factory used a piece of butyl aka "dum-dum" to push the seal out in the very rear corner of the glass. It will fit better if you use some butyl to push the seal out in that area.
3.) Worn out window felts (if you look inside the door this is what the glass rides on. It helps to keep the glass from "flopping" when the window is up, and keeps it from rattling when the window is all the way down) will cause you to have to make more adjustments to the window to get them to fit right. You can adjust these little "felts" up and down to push the glass further in or out when the window is all the way up.
You will do a lot of opening and closing the doors, adjusting the windows over and over again to fit. Don't freak out when you get the windows adjusted right, then you try to roll the windows up with the door closed and they don't roll all the way up. The seals will start to accommodate the windows over time, and your windows will roll up with the door closed.
