I made a homemade GHD as well.
Basically, all I did was take an extra punching bag that I had, which was a small 40lber. You put the punching bag perpendicular on top of your parallettes. Then, I put the adjustable pin in my squat rack such that when I am sitting on top of the punching bag, I can extend my legs out and my ankles will under the pin. Then I just lean back and do my sit ups.
It looks exacltly like Ryan Atkins setup from this page http://www.crossfit.com/discus/messages/26/4355.html
Only instead of the swiss ball accross the parellettes, I have a punching bag. The punching bag allows you to get your butt off the bag unlike the swiss ball and nothing will be under the back of your knees. So far as I can tell, the set up I made perfectly simulates a real ghd machine.