Were the sunroof drains (if equipped) the ones checked? If so, I would still recommend removing the passenger footwell kick panel, should be just a screw or 2 and unclipping from the sheet metal. There you can see in the A pillar where the drain line connects to a rubber elbow that exits exterior of the body behind the front fender. Often times, due to age, this elbow can crack and whilst the drain and line may be clear, the water leaks inside the A pillar and onto the floor. You can stuff the area with paper towels and next rain or hose check see if they remain dry.

The rubber part is NLA, but a suitable rubber hose end can be cut and shoved through the opening to the fender exit and coupled with the drain line.

Presumably to test the rear window leak theory, you could angle the car nose up and see if there is an issue with and without your tape cover. I would imagine that the parcel tray would show signs of wetness up top or below in the trunk from a rear window seal leak.

good luck

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Stable Mates:
1987 300TD 310K mi (Hans)
2008 Jeep Grand Cherokee OM642 165k mi (Benzrokee)