It won't be easy replicating the original rubber lip. It's doable, but it may not look perfectly OEM upon close inspection.
1. Remove molding and strip it clean
2. Clean the glass
3. Replace molding on car
4. Mask off vehicle body (or mask before replacing the molding, being sure not to place tape too close to window so it can be easily and completely removed)
5. Mask off glass down the distance of the OEM lip width — it'll be tricky, as you have to follow the contour with the tape, but it's doable with patience and care
6. Spray the strip down with Flex Seal or similar to the desired thickness
The above should ensure an absolutely flush/tight seal against the glass, as well as an invisible blend with the lip into the molding, since it's all one piece of new rubber.
You could do it off-vehicle by securing heavy weight craft paper roll to the underside of the molding, then mask off the craft paper/board the distance down from the molding that matches the width of the OEM lip (or trim the lip after it dries). The craft paper would follow the contour while being stiff enough not to sag — that's assuming it doesn't absorb the Flex Seal too much. You could use standard, inexpensive craft sheets, but they aren't wide enough, so you'd likely end up with a small sunken line in the new rubber coat where two sheets meet. Unfortunately, rolls aren't cheap.
I plan on doing mine on-vehicle.
If you find that spraying the molding on-vehicle builds up too thick on the molding while trying to build up the lip, you could try a combination: rubber caulk (or gasket maker) first for the lip fill, let that cure, then lay down a thinner coat of Flex Seal over the caulk lip and stripped molding.
If you just want an almost invisible blend, you could paint the molding off-vehicle, reinstall it, then mask the glass and molding and smear black rubber caulk (or gasket maker) in for the new lip and call it done. Not sure how long it'd be before the caulk started separating from the molding, but at least initially this should blend well enough that only close inspection would show the joint.
Last edited by Torque; 05-17-2018 at 08:23 AM.