I seem to recall bending the back loop of the canopy frame up a little bit to get a better fit to the canopy. I also had to bend the forward bow to match the roll bar as per VANs instructions.
In the final fitting, the right side fiberglass skirt fit perfect, but the left one fit poorly in the back 1/3. I cut that part off and laid up a new one in place over sheet plastic and packing tape, using poster board as a mould.