Does it still whistle with the fresh air vents open? non A/C or breathing fresh air from the cowl? A/C. You said the noise was still there when you rolled down the window. If there is no change in whistle then I would suspect it has nothing to do with wind getting in side car (door seals, trunk seals, door panels, windshield, cowl vents, back glass, firewall holes or holes anywhere else into the cabin). You might try using garbage bags to completely block sections of the car for short drives.Also make sure the fenderwell/cowl mud guards are there. Don't forget you can block off front wheelwells with tape and garbage bags also...use the thick ones.
Curt