I think the original reason that Cal sci put the hole there was to reduce turbulence and back pressure on the inferior Gen I FJR's. Because you have the Superior Gen II FJR, this airflow management has already been built into the bike. :yahoo:
Okay, kidding aside, they did actually add airflow on the gen II so it makes it impossible to make direct windshield comparisons between old and new FJR's. I've never tried a Cal sci shield, so can't comment on what effect it has. My stock shield was horrible and I've been much happier with the Vstream for winter use and a Cee Bailey +2 high with flip shield for summer use. Neither is perfect, but I don't think the perfect shield exists.