Hey Cruise Missile.
I agree with putting a bead around the windshield to fill in the gap. I have been through 3 windshields so far on my 2009 Sahara from rock attacks. The most recent windshield I had replaced gave me fits. The gap around the windshield was equally spaced just like the first 2 were, but it started whistling on my way home from getting it replaced. Man, the disappointment you feel after spending $275 on a new windshield and it sounds like Tweety Bird is in your Jeep.
To anyone that has the dreaded whistle, before you go throwing some caulk around,
, tape up the windshield gap first and go for a drive. Like Dale-K shows in a few posts back. Process of elimination is in effect here. If it doesn't whistle with the tape on, remove the tape and caulk the gap. Helps if your Jeep is black, that way you can use black caulking. I imagine clear would look okay too. The windshield gap (approx 4mm or so) around the windshield creates air turbulence, hence causing the dreaded whistle with the windshield. Filling that gap has worked for me. I am sure this method has been talked about prior as a fix.
Just a reminder, this is only one of the areas owners have had issues with the dreaded whistle. Process of elimination should be used to pinpoint the whistle.
I wish you all good luck.