66 window seal replacement question

If they are not willing to do the work, no advice you give them will help. You need to find a restoration shop. Call around and see what they say. THere are many threads on this subj already.
Even with all the suggestions you will find in the search, sometimes they still leak. It becomes a compromise between trying to seal the rubber and creating a HUGE mess.
We will clean the glass completely. Usually wipe down with laquer thinner and clean with glass cleaner. Put a good bead of RTV from a cheese can into the seal and put the seal on the glass. CHeese can the outside of the seal and lay the rope in and install. Keep a rag handy to keep the rope clean as you pull the seal in. You can also go around the outside of the frame with windshield sealer in a chalk gun. Nice thin bead all around and under the moulding clips.
What happens, and we have been through this with a 65 FB retoration, is you can't always tell where the water is coming in. It may seem like the glass, but can be the cowl (especially if not repaired) and can be the drip rails. People overlook the drip rails, but that seam is filled with seam sealer. It gets dryed out and cracks. Even though it may look good, it does not take much water to make a wet spot on the carpet. THe 65 FB had a drip right down the left side of the dash! We never could find it. It was coming out from under the dash pad and just a little drip running down the dash to the left of the inst cluster.
We dig all the seam sealer out of the drip rails in all restorations. After the car gets primed, all the seam sealer is redone. THen primed again. So far that 65 has been the only leak.
Hope that helps. ANd there are probably a hundered different opinions on how to do this. As long as you can stop the water, it works.
Now that you can get a new 65-66 cowl it will be much easier to stop the leaks in that area.