The cowl is all cleaned out. I took a couple of photos and drew arrows of where the leak is. How would you fix this?
I could flex seal around the plastic knob but the second location looks to be a foam gasket, I don't think i can seal that well.
You mentioned around opening in the engine bay. Where would this be you think?That was mostly a joke. Chances are the foam seal between the HVAC box, and the firewall is degraded enough to allow water to go through. You could replace the gasket, but that would be pulling the dash to be able to pull the box. I think a weather sealing rubberized tape along the top edge (or even around the whole opening in the engine bay) would prevent water from coming in.
You might try a dye to see exactly where your water is entering from the outside, and seal that area up.