Underneath the Windshield Cowl. Open the Hood. Remove Wiper Arms. Remove the Plastic Cowling on Both Sides. You will then see the Cabin Air Filter under there. Replace this as it is probably all full of old and mildew. At that point, look in the valley and you will see 2 black plugs. Most likely they are clogged with leaves. Very common concern with mustangs. You can either clean out the plugs and the water will drain outside like it is supposeed to or just remove the 2 plugs. This will ust allow more water to drain faster.
If this does not solve your issue, you have a body seam concern. 95% of the time it is the Drain issue.