So I just drove it around with the temperature thing in mind.
Blasted the A/C for 5 min and it still made the sound.
Then Drove it around for 10 mins with the Heater on and it did seem a bit better, but it is cool at night still so that might defeat the purpose

Then I started playing with that Cowl thingy and it definitely is a huge cause.
I put little tie wraps in between the rubber and windshield and it still pops and creaks when you shake it.
I was hoping it was maybe the rubber rubbing on the glass.
It doesn't do it at all on the passengers side.
I think the Dealer fixed part of my problem with the speaker Grill but I really think it was a 2 part rattle and half is still in full effect........8(
I wish I could figure out how to take this thing over to see if it's that.