Drill a hole in the spare tire well in the trunk.

I know how to fix it!...

Permanently!

I have thought about looking for a good area to drill one, and have even considered a small hole on each side of the floor boards in the rear, I'd have to find some kind of paint, or something to dab on it so the holes to not start to rust.

After using the SikaFlex it seems better, but the rain slacked up a bit so it is hard to tell if it really made a difference.
The more I look at the brake light housing I am wondering how the water gets in there, I replaced the seals around them around a year ago, but water kept getting in to the area right below the bulbs, I'll have to try to get a pic sometime.
The only time they have ever stayed dry was from me putting silicone in the old trunk weatherstrip, and putting it back, of course that did not last long, hopefully the SIkaFlex will fix it again, but last..

After all I did to stop the water getting in the trunk, I go out today and see I left my driver side window down an inch, FML, lol

While out there I did notice something, the rubber stops on each side where not screwed all the way in, I am not sure if they are meant to be unscrewed a little or not, but I screwed them back down, and the trunk seems to close a little tighter..

Water leaks ... open windows ... I think you found the problem.

I don't think sealing the taillight against the sheet metal is as important as making sure the holes the retaining bolts pass through into the trunk aren't leaking. You might want to try a rubber washer on the inside of each taillight nut, perhaps with some silicone between the ID of the washer and the OD of the bolt.

Does your car have a decklid spoiler?

Have you thoroughly examined the rear wheel wells to make sure there are no holes from corrosion?

Leaks come from holes and/or gaps. I think your work on the weather strip has addressed the gaps, so you should focus on holes.

Ha ha, indeed, lol

When I replaced the brake light seals I used a good bit of silicone on each retaining bolt, I tried to find the original parts they used on them, but I was unable to.
That is a good idea to try to find a rubber washer to put on each, I'd have to go to my local hardware store, and take one of the taillight nuts/bolts in to see if they have the right size, then I could add a dab of Sikaflex to it if need be for added protection.
What I find odd is before when I was adding silicone around the seals on the top area of the brake light housing, that is when for a few months the trunk, and the brake light housing stayed totally dry, and we had some hard rains, I'll investigate the area that I put silicone on before, clean it up and use a little Sikaflex instead, as the silicone does not hold up well.

I do not have a spoiler, I have not checked any wheel wells for corrosion, but I don't get any water in there while driving, well I am sure I would, but it happens when the car is just sitting.
We did have a little rain after I sealed the weatherstrip with Sikaflex, and I only noticed like 2 small drops of water in the trunk, that could have fell off of the lid as I opened it though.
There was still a tiny bit more water that got into the brake light housing, I was looking at the area between the brake light lens, and the chrome strip surrounding it, and on the left side I can see black like there is a rubber gasket or something in behind it, but on the left side I can see a little gap around a good portion of it, and I cannot see any black behind it.
Which is odd because I put ever seal back on, I never had to separate the chrome part from the lens though, I am pretty sure it is all one part, it came off that way anyway..

I hate to do it, but I am thinking about ordering a tarp, and some tarp clips, for 65.00 I can get a big enough tarp, and the bungee cords and tarp wind clips I need to make sure it stays on.
That way if worst comes to worst when there are hard rains I can cover it and not have it get an inch or so in each floorboard...

LOL, perfect!

Screw it, I am going to keep chasing leaks, and try to fix them all, but I got a tarp coming just in case I cannot find/stop all leaks.

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With all of that I should be able to stop the water from getting in, and keep it on when it gets windy.
Of course I won't leave it on all of the time, just when it is supposed to rain.
I'll have to be really careful with it so I don't scratch my paint, but I really am due for a new paint job, but I won't get one because my body needs a good bit of work, lots or walnuts or something have hit my hood a lot, looks like I went through a bad hail storm...
If I can get what I need to get done to get a cheaper place to live, and can get this good job I am looking into, then I just may break down and get that Black 2004 SC Park Ave that I have been drooling over...