Where is my Leer leaking from?

We got a pretty good rain last night and I've got some water in my bed that I can't explain. I know it is leaking from the front corners, but this is towards the rear. Car was parked on a slight driver-side rear incline all night for the pics

Leak #1: Drip between the "Tacoma" part of the bed mat and the tailgate. It looks like splashes, so I assume it's coming from on high, as opposed to leaking somewhere else and streaming in. But the headliner isn't wet and I can't find any wet spots around the windows or back glass.
Pics 1-3

Leak #2: Bottom of the tailgate (which I have covered with

$36 ESI ROK BLOCK Tailgate Gap Cover 4.25" width

this, under the plastic tailgate cover). I can see it pooling on the gap cover but I'm not sure how it's getting there. Up under the plastic tailgate cover?
No Pics of this

Leak #3: Back corner piece near where the bed meets the tailgate. This also looks like splashes, but I didn't drive the car at all, so the light splashes there seem weird. It could be coming in on the sides of the tailgate. I have that area sealed with

$28 ESI Ultimate Tailgate Seal with Taper Seal 10ft for use with Truck Caps and Tonneau Covers

this and I don't have any issues on the opposite side of the tailgate, so I'm leaning away from that explanation.
Pic 4

Bonus Question: When I took the plastic tailgate cover off, I wasn't paying attention to the bolts, I thought they were all the same, turns out they aren't. If I try to put the top screw (in pic 5) where it doesn't go it just spins, but never goes any deeper, leaving the head sticking up a good bit from the tailgate. The problem is they don't seem to go anywhere, only the bottom screws seem to go all the way in. Any ideas here?

 

Easiest way to find leaks is with a garden hose.

 

If the rain came in during rain, get it all dried out and climb in the back and have somebody hit it with a hose - preferably while standing on a ladder. You should have an answer within a few minutes.

 

Why didn't I think of the ole water hose trick?

3rd brake light is leaky. Glad it's definitely a Leer issue, will be heading back to the installer next week.

 

Get in side at night and shine a flash light at all seams have someone out side to let u out lol and mark the areas where light can be seen with masking tape

 

This generally works, but they used clear silicone to seal up the holes. Hindsight: use black.

 

I have a leer cap , 2 sets of new windows , and it still leaks a little