Got the particle board floor out, now what?

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Moderator Post (s) for this thread: > Modular renovation by tomh on 07/25/2004

The home was manufactured in 1969. I've removed the particle board floor and paneling in a bedroom. I have a few questions.
1.) Should I replace the insulation in the wall spaces? Some if the insulation is discolored (black)in a few places. I'm not sure what caused that but suspect moisture. The insulation is dry.
Also, I have a 6 inch gap between the underside insulation and the floor. (The height of the floor joists). Should I insulate this space? IF so, to what depth? Should I completely fill the space?
3.) I plan on paneling or putting up drywall. Should I place a sheet of plastic between the interior wall and the insulation to serve as a vapor barrier?
4.) Through the course of removing the floor and paneling, the vapor barrier coating on the floor insulation has been punctured in quite a few places. I am concerned I may have compromised the vapor barrier. Should I repair the punctures? I was thinking duct tape might do the trick. The largest is 3x5 inches. (Major OOPS on that one).
5.)I got started on this because I wanted to replace the carpet. When I removed the old, it became quite apparent the old owners had cats and they had been using this bedroom to spray or urinate. The flooring, bottom of the paneling and some of the wall supports reeked of cat urinespray. I was able to remove the flooring (I had to drill out the flooring from between the bottom of the awls and the floor joists, this leads to another question, see below) and the paneling. Some odor remains on the wall supports. Short of replacing the entire walls, how can I remove the smell? I've saturated the areas with bleach 3 times. The odor diminishes with each application but I worry I may be damaging the wood. Any ideas?
6.) In the course of drilling the floor out between the bottom of the walls and the floor joists, I've punctured the outside metal siding in a few places. What should I use to patch the holes?

I've searched and searched on the internet for answers to these questions..
What an adventure this has been so far. I thought it was going to be just a simple carpet replacement. I should have known better. Two years ago I started to replace a window in my mud room and now have a deck where the mud room used to be.

I'm sure there is a moral to these stories or at the least a memorable quote. I’m beginning to think I should just raise the roof and park a new mobile home underneath it.

(I have other thoughts, but I'm quite sure they wouldn't be as good after deleting the expletives).

Eagerly waiting a response,

Paul T.
Mounds View, MN