I know the pieces that you are talking about.
They are sort of "S" shaped and fasten with a bolt to the top of the inside door frame. The top of the inside door panel should slide between that clip and the window channel. I had the same problem after my car was repainted, seem the body shop took them off and threw them away (only one of a thousand things they screwed up). Anyway, I could not get my door panels to line up either. As I remember, there is one clip at the front of the door and one at the rear, both different. I believe that the rear clip is about twice the size of the front clip. A friend of mine had a door lying around and he gave me a set. You really should try to get the exact right clips. Make sure you don't have two of the same size clips on the other door. I don't think anyone reproduces them so you might want to start looking at the salvage yards. Good Luck