Mark
I had the same issue with my canopy. After the second attempt with aluminum skirts I decided to go the fiberglass route. I have a few pictures on my web site but it is limited. Basicly I just blocked off the gap between the canopy and the skin and then did the fiberglass layups right in place over the canopy. I had the canopy protected so that the fiberglass would not syick to the glass and had the aluminum skin waxed, that way I could remove everything after it cured. I believe I did 3 layups of cloth, removed it, trimed it to size and then used pulled rivets to hold it in place. Then filled over the rivets and finished like any other fiberglass, lots of filling and sanding. I did grind down some of the edge on the plexi where it turns up in the back so that it would lay flat. I am sure I have more pictures if you need them and would be happy to e-mail them to you if you need them.
Pete DeCraene
http://www.ews.uiuc.edu/~decraene/index.htm