Here's my two cents.
First, remove anything bolted to the floor. Sand it down. Apply a primer sealer followed by a "weld through primer". The weld through primer will add a coating of galvinization eliminating a lot of (if not all) rust possibility.
After doing that, rhino-line it. I've also seen good results from Line-X.
Finally, keep the carpet. When you're wheeling and such, keep the carpet rolled up in its box. For daily use and winter, lay the carpet over the floor for better insulation and comfort.
MY CAR:1964 Fairlane 500 4 door, straight six with a T5 speed
Tim's Jeep:'93 YJ, 2.5L, 5 speed, 35s, shackle lift, tow hooks, custom exhaust, relocated mirrors, 3 inch body lift, homemade snorkel, camo valve cover, half cab softtop, TJ rear bumper, etc
Zeb's Jeep:'89 YJ Islander, 4.2L, 5 speed, hardtop and half doors