Ok guys final update and lots of pictures, hopefully this info will be of help to anyone who has leaks in the future.
The car is now water tight and put back together, except for the headliner, as I am waiting for my material to arrive.
Sunroof Drain leaks:
There are 4 drains for the sunroof, one in each corner.
The rear ones the water runs down the sunroof track inside the car, all the way to the back, where the outlets are and the tubes then run down along the rear window and exit behind the rear wheel.
These were plugged so I blew them out with an air compressor. Also, when they were plugged the water would build up enough to run through a slit in the metal track on each corner, which then would cause the water to run on the headliner, down the trim and out under the rear seat. To make sure water is always forced down the tubes if for some reason it was comming in too fast, I sealed these slits up with silicone:
Next you have the front drains. The problematic one is the Drivers side. It runs from the sunroof down along the windshield, behind the dash/firewall and out behind the front wheel.
When running water on the car, I was getting water running right from the corner under the dash where the parking brake is where you can see the cardboard like piece on the floor:
The problem with this sunroof drain is a poor design on GM'* part. The white tube that runs down from the sunroof connects to a black tube further down. There is no clamp on this tube so it simply slips out and all the water then runs into the car.
The connection for this tube if you look at the picture above, is along the side of the car about 5 inches above the top of the parking brake arm. The only way to get at it is pull out the dash, or thanks to the internet, I was able to find another way to get at it by removing the parking brake assembly so you can get at the rubber barrier above it and cut a hole.
When I did that I found this:
I re-attached the hoses and used 2 zip ties to keep them together. They won't be coming loose ever again.
Now that I had my sunroof leaks fixed I needed to turn to the door seal leaks. The rubber seal on the car which the door presses up against when closed, was somehow getting water on the inside of it and then draining into the car.
You can see the water pooled up here where it runs in:
And from the inside it looks like this (This is a picture of the passenger door):
I needed to find out how this water was getting here so I pulled the door panels off and ran a hose over the car once again.
If you look at this picture you can see the rain barrier on the door, which when the water runs in the door it is supposed to then run out of the holes just above the bottom of the rain barrier, however as you can see the seal/caulking on the rain barrier is not tight, so the water then runs out the bottom..resulting in it pooling up on the weather seal and then into the car.
So I got out my silicone again and permanently sealed up the bottom and a few inches up along the sides (if I should need to replace a window regulator I can simply peel it off and then would have to re silicone it again when I am finished)
After doing this I did another leak test and low and behold you could watch the water run inside the door and then out the holes..after opening the doors the seals were bone dry, like they are supposed to be.
I then checked the back doors, which were not leaking into the car, but the seals were still a little wet, so I pulled those panels off and re sealed them up as well. Did another leak test and now the door seals are completely dry.
The trunk leak I looked into and a simple thing that caught my eye was the plastic molding that runs along the bottom, which has an opening where water can run down in, so I put silicone on those to seal them up as well and that seemed to solve my trunk leak problem:
So now the car is water tight and I can start putting it back together.
Before I did that though, I wanted to protect myself one step further from having to rip everything out again if for whatever reason some water would work its way into the car again. I decided to seal up the foam on the underside of the carpet so that if water would get on the floorboards it would not easily soak into the foam, as it took me 3 days of fans, sitting in the hot sun, and squishing, to get the foam dry and water free..something I don't want to have to do again.
So I glued plastic to the bottom to prevent it from soaking water.. I also drilled a small hole in the corner of each rear floorboard where the water liked to pool up and painted the drill holes to keep from any rust forming (even here in Florida). This should make sure any water that gets in won't pool up and will drip out the bottomI didn't remember to get pictures of the drill holes though. It may work, it may not, but I feel better that I took this extra step. :
While I had everything out, the headliner was loose in a few places so I decided it would be a good time to replace that. Here you can see I have the fabric removed and am half done removing the old foam backing of the fabric from the headliner board:
I finished that up and it is ready for the new material, once it arrives I will finish it up and then that will be the last thing to be put into the car..for now the car functions just fine without it.
And here is how it looked without anything in the car other than the dash itself:
And for anyone who wants to know how to remove the backrest, after removing the bolts on the bottom, there are 4 clips that hold it in near the top:
Simply pull the seat out enough from the top so you can see the clips from above and use a flat head screwdriver and push the tops of the clips down to compress them so that you can pop them out.
I hope this will be of some help to the next guy who has water coming into his car. Also I hope it can help prevent issues for some people, go run water on your cars..if your door seals are wet, then water is getting into your car, even if you don't see it...so you need to fix the seals on the rain barrier inside the door. Your carpet might not be wet, but I guarantee the foam on the underside of your carpet is..so do yourself a favor and fix the problem before it becomes a mold infested, horribly smelly issue