This is a HUGE job and is beyond most do-it-yourself people without causing damage to the trim. If you really feel the need, e-mail me and maybe I can help. I only check this forum once every week so please be patient for a response.
the best thing to do is take your time. look for hidden bolts. mostly they(trim pieces) are clipped in. watch for the retainers as they may come loose, stay in vehicle or break off. you will need to remove the a, b, and c pillar trim. the light bezels will be next. your sunroof trim(i assume you have that since you are looking for water damage). this is a big deal and will take time. just to let you know, the body is painted galvinized so i doubt you have to worry about rust. if there is damage to the liner, you would see that i am sure.
Why are you doing this yourself? If the windshield was replaced, the shop that did it should be willing to verify if it is leaking or not. Do you have too many miles to have the dealer check this under warranty? Sorry, I fix million dollar machines for a living, and wouldn't do this unless I was out of warranty. Just my thoughts. Good luck no mater what you decide.