Check the sunroof drains. With the glass removed, run a water hose very slowly to pour into the pan around the perimeter. There are four drains in that pan, one at each corner, with a hose leading down each nearby pillar post(the A and B pillars). Water should not pool up in that pan, and you should see a solid flow of water below each pillar where the water is filled at.
The cargo area glass can be sealed from the outside, if you don't mind a thin line of RTV visible. I've done it a few times, almost all of them will leak eventually. If you are fine with that, just run some cheap tape along the top edge of the cargo glass, outside. Tape off the seam where the glass rubber trim meets the body, leave the tape about 1/8" from the rubber, so 1/8" of paint shows. The tape on the rubber you can make it 1/4" or so from the paint seam. Spread a very thin layer of Ultra Black RTV between the tape, smoothly as you can. The leak is usually along the top or one of the top corners. So taping it off including the top corners is a good idea.
That works well and will last for many many years, but if the sight of a strip of RTV bothers you, yank the interior trim and pull the glass out. I've done this because it's very quick and works. I had removed four of the cargo glass before, rebuilding two Explorers. So I was familiar with the time and difficulty of R&Ring the quarter glass. It's not hard, but it's not fun either.
