water leak

I picked up a gorgeous 99' 2.8 and have found some of the usual water/leak issues. Pads under carpet are pretty soaked and there was about a 1/4" of water in the battery well. I'm getting ready to take out the carpet and clean the foam underside. I was also working on the glove box sag repair...

I'm currently in the process of hunting down a rather large water leak, the passenger side carpet was saturated and I could hear the water moving around under it. I've found water leaking in through both door membranes, so I have bought some new OEM membranes. What sort of sealant or adhesive...