When I did mine the diaphram had a long pigtail that you could grab with a pair of needlenose pliers and pull through until its seated. Then you just snip the end of the tail off and its done...Also I THINK the diaphrams only go in properly one way...Also, the diaphram cover has the arm with 2 holes in it...make sure the activating rod is in the INSIDE hole.
What brand of kit did you get ??? The Motorcraft kit is still available from Ford last I checked...CT499D p/n D4AZ9A586A


- cs65