When I did mine, I cut cotter pins in half, and bent them with pliers using the existing holes from the staples that I removed. The cotter pins I used were the same diameter as the staples I removed. This may not be the most correct way of doing it, but they are still on the car after a couple years so far.
I got staples from Willcox and drilled holes through both the door panel steel and the backing for the window felt. Put the staples in and used needle nose pliers to bend the ends over. It worked well.