Help: Interior Troubles

[IdahoMan]

Hi all.

I'm concerned about my interior. There are leaks and some bubbling under the carpet by the kick-panel. I've decided I'm going to tackle the entire interior, but I need some advice. For instance: What should be replaced or if it is better off left alone or restored OEM.

Here are pics: (if you need a pic, just ask)

There's some orange in the highlighted pic, that worries me (it's the base of the windshield above the glove-box). My new windshield gasket has always been a problem. Large gaps between it and the body. You can see the water trickle behind the kick-panel. In the last pic, the hole to the right seems to go straight through to the outside. Is it supposed to be like that?