I had the same problem. Water came in from numerous places, mostly through the blower housing. Turns out, in my case, the deflector cover under the cowl that covers the fresh air opening for the HVAC, is supposed to have thin rubber inserts where the push pins cover the panel that goes over that. They rotted out. I used some rubber plugs that we normally use to cover bleeder screws on calipers and wheel cylinders. Push one through the hole then insert the push pin into that. It sealed very well.
The other place I had a leak was near the right lower corner of the windshield where they use body sealer to cover a seam of 4 panels coming together there. The seam sealer had gotten old and brittle and cracked leaking water inside just below the A pillar. I chipped away all the old seam sealer and used some RTV to reseal the entire area, making sure to push it into the seams for a good seal. So far, no leaks. Good luck.