Ok an update!
Jesse the manager from Gates has gone out of his way to fix the problems. Everything now has been fixed on my car with a 100% promise that their work is up to par!
As a "I'm sorry" I even received a gift card to Red Robin, dinner on Gates, showing me that they cared for me as a customer.
The shotty collision repairs were not excusable, and since I had to be the one to point them out, this was not acceptable.
I will still say my time was wasted fighting with Gates and Progressive about this, and it still was a horrible experience. But, thank you Gates Auto for making things right in the end result on your buck!