For sure get rid of all carpet. After five years in the garage the '90 Bronco I'm restoring (or building, depending how you look at it) still had moisture under the rubber carpet. I did spray the floor with Gatorguard, right after I painted the floor with POR 15. I too am going to do something different with the interior...I'm going to replace all factory pieces with thin wall aluminum diamond plate and incorporate "tool boxes". The door panels will be a bit of a pain, but I think it will work.
The Hauler - '05 F-350 4x4 CC Dually 6.0 Powerstroke
The Project - '90 Ford Bronco 4x4
The wife's - '11 Ford Escape
For every minute you are away from work...you can add two minutes to your life!