There is a rubber flap that between the black edging and the body of the car around both front windows. Is this something that can be cut out or is this something that I should have looked at?

 

I'm pretty sure I know what you are talking about but pictures would be nice... And why would you want to cut it?

 

You mean that a little flap is sticking up from the area between the window trim and the body? That happens to alot of us. Something to do with improper installation from Ford. There is a thread on how to remove the trim and replace the stuff floating around somewhere. I don't have the time to search around for it right now, but someone else might have the link.

 

Yep, thats covered in a TSB.
Push it back in with a CreditCard.
Or get the new improved ones
from Ford and replace them.
I got water intrusion because
of it and did the TSB "upgrade".