Butchered hvac case.
The case when sealed will drain through the firewall:

 

Does the drain have a rubber hose that does a 90 degree turn, if so I did locate that one. All is clear there. I wonder it the foam around the top failed and is allowing water past it into the box?

 

If it leaks in against the firewall, replace the case mount seals:

 

Sounds like a long tedious fix. But to get it right with now water would be awesome. Do you have a part# for this kit?

 

Another question, is this a complete dash removal to get to the a/c box to change these parts?

 

 

Yes, you need to remove the hvac case to seal against the firewall. If water leaked into the case it would drain out through the firewall, yet looking at the condition of your case, it could be the source of water intrusion into the cabin.

 

So you are saying the dash needs to come out all the way or can the a/c box come out from under the pass side? Do you have a part# for this or where I can find it? Thank you for all your help.

 

I found the part kit. Unfortunately it is no longer available. That is not what I wanted to find. What exactly do the filter covers do? Do they keep out water while allowing air to enter? So my next option is going to be cut the cowl open and build something to channel the water away from those ducts. It's about the only option I can see moving forward. If someone has a better idea, I am all ears.

 

THAT'S what your Alpha looked like BEFORE you bought it? I would have turned and run!!