I can tell ya, an inch is allowable. Working at car dealerships for around 8 years, many warranty issues came up, but an inch in the door is allowable. I thought this was retarded, but oh well. Best you can do is get new belt mldgs, inside and out, drill holes in the bottom of your door if possible.
most factory speaker come with a baffle that covers the top half and the back of the speaker so water runs down the window and hits the baffle and drips off the back, that good enough for them
My advise...get the speakers out of the doors and into some kick pods.
I have a 3 way front stage for my current project. The mids and tweets in kicks and 8s in the doors. The 8s will be fully enclosed in a plastic custom sealed enclosure that will be mounted in the doors. Fully sealed=no possibility of water/moisture damage.