So I've just noticed a leak in my driver-side rear cargo area. I recently built a drawer setup and I'm using the rear cargo area way more, so I'm just noticing it.

Not sure if it is leaking somewhere and the running across the ceiling panel and coming out the rear where the cargo light is, or if that's where its leaking from the roof.

My sunroof stopped working long ago so it has been sealed up with silicone. The roof rails came off when I wrapped the roof but I just pulled it back off and siliconed the hell out of the bolt holes before replacing it. I also resealed where the rear cargo door wiring harness goes into the body. The windshield seal looks fine but it hasn't been replaced in over a decade.

AND IT'S STILL LEAKING. Quite a bit.

Is there anywhere else I could have missed? Driving me nuts.

It has 4 drains from the factory starting at the corners of sunroof. When they get clogged, they leak inside vehicle.

I found water and mildew in the cargo area when I swapped my carpet. Easiest way is remove the headliner but is most time consuming.

You can check the sunroof drains and see above without removing the headliner, maybe your silicone seal-up job has partially failed. The front drains run down the A pillars, remove the lower trim pieces, pull them up and run weed whacker line up through them. The rears are above the back doors toward the back of the door opening. Pull back all trim around the top of the door, remove the Oh Shit handles and you can pull the side of the headliner down enough to see it with a flashlight. I was able to get my hand in far enough to stick a thin screwdriver in the drain hole to clear it. Would have been helpful to have a kid or my wife with smaller hands do it but it's possible with man hands.
That's how I found a drain line that wasn't connected at all.

Also maybe check your rear drains are actually going down and out and not dumping back into the cargo area. Timmy the Toolman has a good video on the drains and how they're routed and how to clean them.

I also had leaks in my roof rack bolts, removed the rack and siliconed those MFer's then reinstalled.

Dry as the AZ desert now.