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Have a 69 C3. Just got done putting on the outer seal and blasted the tracks and repainted so they are very clean. When I put in the window and felt on the backside I had to push the bumpers against the glass quite a bit to get the seal on the window on the outside. Because I have it pushed so tight it is making it hard for the window to go all the way up without assistance by pulling up on it. Is this normal? Is it my motor? The motor seems to work well, just not sure if a new one is more powerful.
There's two pieces to the outer window seal. The chrome strip on the outside and the felt or rubber strip on the inside. The rubber strip has numerous 'buttons' that have to 'plug' and snap into the holes in the door. There should definitely be a 'snap' when you push each button into place. If there isn't, then you need to pull the felt and gently spread the two halves of the 'button' outwards.
With the glass in place, even down to the bottom, it was difficult to snap the buttons on the felt, but I came up with a trick (don't push on the glass!!!). Using the Lisle upholstery tool, I put the backside of it against the felt (didn't even have to touch the glass) and applied pressure, pushing it in, like so. They snapped right in.
The felt should be totally flush. If there's a gap, check and see why. Also, you may need to adjust the window bumpers as well. And as Easy Mike said, you may have adjustments to do. A good starting point, before you even adjust the window, is to make sure all the bolts in the door are in the exact same place you removed them from!