Those clips "might" be after-thoughts to fasten the window runner felt to the door. I've read that some guys put a couple screws through that channel felt to keep it in place.....but mine stayed fine. I just did this entire operation today and after 10 hours on the one door, the second took 2 hours. I can help you get it done in 2 hours too!
I'm posting it on my blog right now. Check it out shortly:
http://e-tekrestorations.blogspot.com/My site:
www.E-tekRestorations.com