What year model of window felts did you purchase them for? As has been mentioned above, the 70 model used clips to hold the front door felts in place while in 71 and up, the door felts used an Auveco 672 screw. It sounds as if bought the 71 to 74 style felts, yet the door skin was a 70 skin. After being involved with the Topcat window felts for over 20 years, it is very common to find guys who find out that the doors have been swapped out over the years on their car.
The simplest means to alleviate this problem is to carefully bend the tabs that hold the clips in place to the window felt. Once the two tabs are bent up, flip the felt up and then carefully pry the clip from the felt. Then do this for the remainder of the clips. Once all of the clips are removed, roll the door glass all the way down and position the felt in place. Rock the felt slightly so that you can view the attaching holes and use a silver Sharpie, mark the location of the holes in relationship to the felts. This should get you very close to the approximate position of the attaching holes. Then take a sharp awl and punch the screw holes. You can drill them, but be careful not to allow the felt to twist as you hold it or it will bend.
Hope that this is a work around for you. I prefer not to bust up sets as the raw material is custom cut so as to eliminate waste and to maximize kit pieces from a single piece of material. If more questions, drop me a message.
