If you're referring to the "fuzzies" that attach to the door on both sides of the glass - they should be about 1/2" tall and mount almost flush with the top edge of the opening. I installed new ones on my 1960 GMC about 10 years ago, and they were a bit snug for a while but fit well right from the start.
It sounds like you were either sold inferior parts or the wrong ones for your truck.
