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Cut it at the top. It's a straight cut and you won't have to follow the complicated contours of the bottom.
If you must cut the bottom I suggest the following:
Create a copy of the bottom contours by tracing onto another piece of plastic or similar material.
Cut that closely with your jig saw. Clamp to your windshield and trim with a finish router.
Now use the copy in the same way to cut your windshield in the new location.
Do a search on this site and you'll find lots of good information about cutting and finishing your shield. Most do it at the top.
rotozip works, band saw as well. I would "polish" the edge you trim just to prevent cracking. Sometimes the plastic will "wick" any kind of petroleum product that may be lurking in your fairing and cause cracks if you don't polish it off a bit. good luck! : )
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