Water Leak Problem

Hey guys, newbie here.
I've been having a helluva time with a 2000 X we picked up recently.
I'm getting leaks at the 2nd row doors and the carpet soaks it up like a wick.
A similar problem is happening in the back door area.
The weatherstrip appears to be in good shape.
I've pulled the carpet up once already and now it looks like I need to do it again.
Anybody else experience this too?
My current plan is to pull and reinstalll the weatherstrip with silicone adhesive at the flange where it pushes on.
Any opinions?

I don't know about the side doors, but I do know what is going on in the back. The back needs to have the carpet pulled up. After you pull the carpet up, you'll find that there is holes in the frame. If you look through these holes, most likely you can see down onto the road. When it hits rainy seasons, the tires throw the water up and it soaks the carpet from underneath. It's not the weather stripping. The only way you can rectify this is by sealing up the small holes with a sealant of some sort. Also, there are black plastic rectangular shaped seales covering up the biggest holes. Most likely these are warped from the weather and also need to have some sort of sealant or caulking placed around them to keep any water from seeping through.