Air vents open for the flies?? Close them and see if that sorts out the fly problem, if not.. Look about for either holes or a nest.
As for the whistling, might not be the vents.. There is a small hole underneath the driver mirror, might be this or your wipers, venting is usually not open to elements as there are filters in place to stop this.. But if it is, check underneath the bonnet under the plastic grill between the windscreen, wipers and bonnet (careful when removing the plastic screws) the rest of the venting is underneath the dashboard/behind centre console. If it's internal, switch the blower on full and check for whistles.. My money is on the mirror hole/wipers though. The hole underneath is just moulding due to outside temp sensor as it's on the passenger side. sealant will stop that.