I know what you mean if there is too much material the piece will not sit down all the way on the car. I have wrapped them around so the material tucked under on both sides, but like you suggested the piece fits odd. This last tr3 I took apart the material on the inside of the door capping DID NOT tuck under on the inner door side but did on the outside. I believe this correct from the factory, but not sure. The outside would have to tuck under to make a weather seal, but the inside could finish being behind the door panel and not have all the buildup of material.
I also used Geo wooden deal, but I did not soak them in water. I basically waited for hot July day and also used a heat gun. I moved very slow and divided the gluing up into sections. I glued the top face first at the one end of the dog leg in that big dip and let that sit overnight then move down the top of the piece and glued that and glued a little down both sides let sit overnight--- then did the last dog leg and let that sit then work the material around the sides and ends