Was getting a lot of water coming in during heavy rain. My fear was the fresh air intake under the cowl. I ran a hoe down there and everything drained as it should. Then started checking other areas and narrowed it down to the bottom of the blower motor. I used some permatex marine adhesive/sealant at the low point of the blower motor. Let that dry and was still getting a leak. Got some water sealing tape (Nashua brand). Put that over top of the permatex. Pain in the butt to get your hands in there with tape that sticks to itself. Still no luck. Last resort was to make a gutter to keep the water from even dripping onto the blower motor. Looked around the garage and found a shampoo bottle that was the right width. Cut it in half, used the water tape to tape the two halves together and then tape that to the lip of the engine compartment. Totally ghetto but worked.
I don't really see that the blower motor has any air intake besides the fresh air intake under the cowl. Seems like I could just find a way to cover the whole motor assembly and be done with the problem. Maybe a half sphere kind of thing from a tupperware bowl. I saw several threads on this topic with various solutions. This is ghetto for sure, but if it helps someone solve the problem quicker then it was worth it. I'll definitely get back to this. In my case, the problem seems to be worse since I park it uphill. I was trying ot park it pointing downhill, but apparently this is too difficult for other members of the household that drive the jeep.

 

I had the same problem but instead of sealing the blower, which I see as a symptom of the real problem: water getting into the engine bay, I sealed the seam at the top of the firewall so that water can’t get to the blower motor. Treat the PROBLEM, not the SYMPTOM.

After pouring water into the wiper cowl, it leaked into the engine bay through this seam. RTV at the seam fixed the problem.