Sorry for jumping onto this thread +2yrs late but I just experienced all of what is being talked about in this thread.
Jon is quite correct in that the leaks that I have found in the rear were not caused by the sliding split window (no physical ingress to the interior by the window) but by the trim piece below it; there's 4 plastic clips with little rubber hole gaskets that are supposed to keep water out but over time they dry out and water leaks in and onto the pedestal jack and will soak the cargo deck matt, that's your tell. Be careful when pulling the trim piece, it's thin aluminum and the clips are plastic, so it will deform easily and the clips will either stay in, detach, or break, and mine had a lot of mung under it. Silicon or RTV around the holes and under them in the quarter panel works; I used marine grade 3M trim sealant, but that's just me in Seattle where it rains a lot.
For the sliders in the rear, I was replacing the outer gasket and inner slide gasket and they are an amazing bear in how they seal with overlapping rubber to keep the water out. I used bicycle tyre irons to help and cord to re-fit them in. I spoke to my dealer and the whole glass panels are still available with gaskets for pretty reasonable, and as Ecoman pointed out, you will have to replace the rear cargo vent covers (8mm stud with 2 clips) and they're pricey for what you get; I sealed the areas around the body clips and the cargo vent as you cannot access these from inside the vehicle just to make sure they stayed water-tight. I'm still debating on the whole glass option as I don't use the sliders anymore and I'm always worried about someone prying open/breaking the slider.
Thank you all for all of your tips and insights!