Thanks for the pics Brian. I'm considering the same mod for my 06 (Home Depot version of Lexan) as I currently have the stock windshield on.
Jeff
I think I'd use clamps to hold the Lexan to the OEM screen and trace directly if I were to try it again. No 2-step with paper (clearly didn't work for me that well).
When installing/drilling the holes, I located the center 2 at the bottom first, drilled a pilot and then the main hole (sloooow speed cuts right through, nice and clean). Then I alternated to either side and just bent it back a little at a time to mark and drill the next hole. Everything lines up nicely, it was a "first time's a charm" deal with the screw holes.
Wish I could give a ride report, but I blew a chunk out of my valve cover gasket yesterday so the bike is torn apart waiting on USPS to deliver a new one from Murphs...