Hey Drew, good to see you posting on here! You inspected my bike for record cert at BUB 2007. You did a great job, because you passed it!
I have had to heavily modify the Air Tech fairings that I bought. I tried various methods (shears, jig saw, haw saw blade) that made a mess. But the best and cleanest is using a electric or air driven cut off saw with the smallest and thinest fiber blade you can get. The smaller blade makes curving the cut easier. Mark the lines where you want to cut, then make a few passes along the lines (don't plunge all the way through the material.) You can easily avoid burning the resin and glass by making several shallow cuts on the line. That way it is easy to make curved cuts.
But there is a new tool out that I want to try. It is the dual saw with counter rotating blades. It claimes the cut is neat in all material, even steel.
http://www.dualsaw.comGood luck. See you at BUB.
Don