'85 380SE, same problem. I get water in both wells, left and right of spare tire well. I've ruled out the trunk weatherstrip, as I can't see any penetration anywhere.
I ran a good bead of silicone under the sides and bottom rubber flanges of the rear window seal too, thinking it was seeping in somewhere around the sides/bottom of the glass (BTW, glass was replaced last year, bad delamination both corners, but they re-used the old rubber seal. The new glass wasn't OEM and a bit thinner I thought, so may not have sealed properly) Didn't help.
There's a water drain hole in the bottom of both wells in my model. The left one accomodates the drain tube from the power antenna, which the lack of, or positioning of, may be your problem, especially if you have a non-original power antenna that either lacks this tube or fits poorly at the fender grommet.
I believe my sunroof drains exit at the rear of the rear wheel wells, outside the trunk, so are not suspect. All I can think of now is to get inside the trunk and have my son spray the area liberally with the garden hose. Maybe I can see where it's coming from if the carpet liners are out....but that may not happen until spring. Hope my comments help.

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1986 560SL
2002 Toyota Camry
1993 Lexus