All other fitting is done first, canopy to frame, rear and side skirts, closure, skirt stiffeners, the whole ball of wax. THEN notch the side skirt as required to just clear and parallel the deck. Do not use your notch as an index. Otherwise, proper skirt fitting will be next to impossible as you're dealing with a slight compound curve for all skirts, the metal will shift considerably during fitting, and the notch clearance will slop around. The notch is a trivial feature to implement once all else is done. I highly recommend you get fresh material and start over.
This procedure requires removing the skirts (un-clecoing)if you want to slide the works open, but so be it.
The windshield is fitted to the final canopy position, shimmed as required. Do not install it until the canopy is completely fitted.
John (Six Sliders) Siebold