There are several determinig factors which need to be clarified before you can proceed with any success. First off if your using new glass, it will never seal as good as the originals and some new glass (depending on the manufacturer) is way off. If your using new aftermarket channels, same deal. And last but certainly not least, the seals. As the old saying goes.... nothing is as good as the original. That's true, but you should be able to adjust your windows to get rid of most of the wind noise. The new seals are great, but any changes to the doors, body, etc plus the passage of time and less accurate tolerances from when these cars were manufactured is working against you.
The door and quarter glass are very adjustable in the top and bottom stops, fore/aft and tilt directions. Allow yourself plenty of time and a few cold ones
. You'll be opening and closing the doors and rolling your windows up and down quite a bit. The tilt is controlled by two plates (one towards the front and one to the rear) of the door glass. These plates are part of the front and rear tracks and face towards the sky. You'll see the slots. Moving them in or out will change the tilt. The fore/aft adjustment is controlled by two angled slots around the center of the door in the area of the arm rest. The slots are punched out of the inner door structure and will be facing out. The top stops also can be adjusted to cant the glass for a better fit. You'll be playing for a while so be patient. The quarter glass has the same type of adjustments. The nut and slotted stud at the bottom will control tilt. The number "7" shaped slots control the fore/aft as well as in/out by adjusting the slotted studs. Just remember to make sure you don't over adjust the glass to where it doesn't fit properly against the quarter glass seal.
You may also have to play with the channels themselves and move them in or out to meet the glass better. Keep playing and you'll get a much better seal. Be patient and be sure to mark your original locations before you start so if you get lost, you can go back to square one. It may sound intimidating, but its not too bad, just real time consuming.