Read more about the Front leak solution on 2005, 2006, 2007, 2008 and 2009 Ford Mustang V6 4.0 and V8 GTs resulting from the cabin air filter area coming through the glovebox.
So my car started doing that mysterious leak thing again, with water coming in from somewhere under the glovebox. My dad and I found the TSB and checked all the spots they recommended. Weather stripping was intact, etc. Then we decided to pull off the vent on the top and look underneath by the cabin air filter. That's where we found the leak - here's what we did with a few pictures.
This is the area after taking off the black plastic vent:

There was a lovely amount of water in there:

So we wet-vac'd the water out and soaked the rest up with paper towels. Then we pulled out this rubber drain in the cowl, which was clogged to the max with lots of gunk.
This is the drain (cleaned out):

And this is the slot where it sits:
So that's the process. We took off the plastic vent panel on the passenger side, soaked up all the water with a wet vac and paper towels. Then we took off the cabin air (it was soaked) and cleaned out the gunk from the drain. We then replaced the drain, changed the cabin air filter to a fresh one, and replaced all the necessary parts. I think that should stop the leak and hopefully this will help anyone else out that's having this problem!