My wife has a 2004 rubicon and now that we have put her hard top back on the thing whistlles like crazy on the highway at 65 miles per hour. Any thing come to mind on how to fix it? I sure would be forever grateful.

 

A whistle is caused by a deflection in the air stream. It has to be something with the way the hardtop is fitting. Either there is an air gap or there is something sticking out like a seal. A pinched seal, that is pushed out, will do it too.. A real close inspection and you should be able to find it.
Look closely around the windshield and at the top front of the doors. Don't forget to check the back side of the front door to the door jam where the hardtop meets too

 

I wish my hard top whistled, I'm tired of singing by myself. JK.