The fiberglass layup turned out to be a non event. If you have gone this far making the fiberglass layup for the canopy is no big deal. Follow the insturctions and you are good to go.
I have seen the prefab windshield fairing and was not very impressed. It is very thin and IMO, flimsy. Once I saw it, I was glad I chose to do the layup. As Geico said, it's a non-issue. Just stop thinking about it and do it. I think you will surprise your self.
I enjoyed the canopy layup. It was a nice break from the aluminum and I felt good about actually making something instead of simply assembling. It was satisfying for me. Follow the plans and I bet you will do fine.