I'm going to start stripping the wheel well housings and frame, any ideas of what to use to coat these areas? Looks like the wheel wells were factory coated. Whats the best way to strip these areas? Do you guys use rubberized under coating?

There's no easy way to remove undercoating. Best shade tree method I've used is a propane torch to heat it/soften it, and a good old paint scraper. Keep a fire extinguisher handy and be prepared for a messy job like you've never seen.

On the replacement coating, it depends on what level car you are building. The OE show guys have a pretty complex process of replicating the factory undercoating both in material and spray pattern.