Leak in cowl

Wondering if I’m having the same issue. I’ve been dealing with the common water leaks on both driver and passenger sides but only when I let the truck sit in the rain for awhile water somehow manages to get inside my ecu and fry it! Truck won’t start until I let it dry out a day or two before it runs again. My theory is that the water is running along/inside the wiring harness loom then feeding into the ecu itself. I have the edges and corners of the ecu taped so water can’t be getting inside that way.
The wiring harness is relatively high up inside the dash, higher than where I believe most of these leaks usually come from. A bad windshield seal is starting to make more and more sense to me. Would be a helluva lot easier to fix too.

 

Thursday morning, I visited a local glass repair shop. He ran water over the suspect areas, and it was watertight, he couldn't identify a leak.

I'm having the windshield replaced Monday morning and believe it'll seal the leaks. It has a chip that's big enough to warrant replacement.

Next time it rains a lot I'll leave it outside the garage, and I'll report the results.

 

The windshield is replaced. The old windshield seal didn't reveal any obvious leaks. Last night I left the truck outside while it rained about 3/4". Today the driver's side floor is dry, so maybe my leak is fixed.
Today I removed two bolts on each side holding the fender, that screws into the cowl area. I applied thread sealant and put them back in.
The two bolts, on each side, that hold the hood hinges to the cowl area are unaccusable without moving the fender out of the way. How hard is it to loosen the fender so I can apply sealant to those bolts?

 

Have you tried running water down the rear of the cab between the bed and cab? I had a rubber plug in the rear that leaked and the water ran all the way down and pooled under the driver's side front carpet. It was really odd.

 

Had the same thing happen back there. Also I had to take off the wiper cowl and run Flex Seal along the inner seam where the cowl meets up with the firewall. Here's the writeup that I followed when doing mine: https://www.tacomaworld.com/threads/passenger-floor-board-leak-fix.432290/. I didn't take off the fender or wiper motor in my case, although it would make it way easier. I'm just double-jointed so I was able to twist my arm inside of it with a paintbrush lol.

 

Yesterday evening the truck sat outside with ~ 3/4" of rain.
The driver's side, if it leaked it was very little. I cannot decide of the carpet is wet or not.
The passenger side has a little water on top of the Weathertech floor cover near the RH edge. Removing the Weathertech I see the carpet is wet near the door opening and the kick panel. Seems maybe it's coming in through the door seal at the A pillar. In reading the @HoneyBadger153 link above it might be coming through the wiper channel at the base of the windshield.
I now have a nice, new clear windshield but the leaks remain.

 

I had my floor getting soaked, found it was coming from the cowling. Parked downhill, put a hose inside that channel and it poured in.

 

This is exactly what mine looks like. It helps if you pull the carpet all the way back up to the seat bolts too. Remove the shifter plastic, center console, and lower dash garnish, and then the hose test will be a lot easier. You can see exactly when the water is coming in and how much since it's not getting absorbed by the carpet.
At some point I'd like to do an ozone treatment since the insulation against the firewall was wet. Rest of the carpet was pulled out, repadded, and steam cleaned. Can't get rid of the musty smell though due to that firewall padding.

 

I found that after replacing the floor pan, which I’m assuming was the cause of the rust. That factory insulation was nasty. I replaced it all with sound deadening and then took the carpet to the car wash, degreased and pressure washed. Looks great now!!

 

Insulation was a total pain to remove too. Almost like they coated the bottom of the carpet in glue or resin, then applied the padding before it cured. Definitely would recommend lifting the carpet up for a few days and spraying it with vinegar/water mix to kill any mildew if you haven't already, OP.

 

Recently the truck sat outside during a heavy rain. I noted the passenger side floor was pretty wet under the WeatherTec floor mat, and could see a water trail coming from the door area. I remembered that years ago I applied sound deadening to the inside door panels and perhaps I didn't seal them well.
Sunday I pulled off the door panel and found the access hole in the inside panel was mostly open. This might allow water to flow past the door glass, and spill over to inside the door panel, then drain into the truck. So I used some thick plastic to seal this area. While at it, I removed the driver's side door panel and ensured it too is water tight.
More rain last night. Let's hope it's now sealed up.

 

If the sheet fell down you may have an issue with the black butyl adhesive being dirty or dried up, so adding just new plastic might not be the "forever fix". Amazon sells rolls of it (13 ft roll did 3 1/2 of my 4 doors for the double cab), but you have to heat the old stuff up with a heat gun and scrape it all off (take a picture beforehand of the old tape to re-create it) then use some Goo Gone or whatever to remove the leftover residue. When installing the new stuff, make sure it's heated and there are NO wrinkles in the plastic where it meets the adhesive or ANY gaps or cuts in the tape except for where the original tape left gaps. Use a good waterproof packing tape for the wire harness passthrough and water drain gaps at the bottom of the doors. Remember, water has to hit that sheet and flow down so it needs somewhere to drain to - that should be where the packing tape spot is. I used a cheap plastic wallpaper roller to affix the plastic to the adhesive while heating with the gun which worked really well. Make sure the mating surface between the metal, tape, and plastic is completely clean too when doing this.
This whole thing took a solid weekend (all 4 doors though) between cleaning the old tape off and slowly applying the new sheets and putting everything back together. 1 year later and 0 leaks so for ~$20 in supplies it was definitely worth it. It's definitely fixable

Also, you didn't happen to modify the black speaker housings in the doors, did you? Those are designed to guide water away from the opening as well as from leaking through the speaker cone itself, so any cuts to the plastic will likely lead to water ingress.