OK here it goes.I had to remove the passenger front seat, the crash sensor, to allow room for a caulking gun to seal the seam betwwen the floor pan and the A and B pillars, these are the first two pillars you need to pull the rug out of the way as much as possible. Then against the firewall there is a rubber mat that must be lifted high enough to seal this seam. I bought two types of silicone sealer, one is the standard 100% silicone, the other can be found at Advance auto parts, it called flowable silicone. Buy 3 or 4 tubes, they are small tubes! The crash sensor is on the passenger kick panel under the rug, the plastic trim just pulls up, then back away from the pillar. This sensor must be unscrewed from the pillar like I said. Under the sensor you will see a rubber insulating mat, under that if you find water comming in from there you also need to remove the rubber door seal and seal the welded seam, this is were the flowable silicone comes in handy! Also I cleaned this area first, and around the windshield seal. Get that flowable sealer in the space from the top corner of the winshield all the way to the bottom, then lift the bottom part of the seal and apply regular silicone under it. The rugs have a sponge like material that holds a ton of water so use a wet vacuum and remove some floor pan plugs to get rid of the water. I also used a heat gun to help dry it out. I sanded the rust spots and filled all holes with bondo, and repainted! Now the second part of the problem is the rain hat. That is under the hood under the right windshield wiper. Remove the two plastic screws pull the rain hat off, remove the seven screws holding the air intake for the a/c system, Water gets in there as well! Remove the sponge gasket, I went for overkill here, and bought a couple of rolls of cork gasket sheet. I made three gaskets and used 3M part number 08001 super weatherstip adhesive and gasket cement, Coat both sides of each gasket, aloow them to dry for 5-10 mins, then one by one put them were the old gasket was.
Now put a bead of silicone on the last one and put the part back on the car! I did this because even tho I tried silicone only first, it did not completely seal it!
Then go here for pictures on how to seal the rain hat.