The channels(inside part) could be made fairly easy.
I had 0 rust in the well. Only rust I had was on the lip of the well to the fender.
If you search around in here you will see repairs done to well wheels. Especially around the rear seat bracket area(bad areas on BJs)
post up some pics of the rust. Depends where it is. Some areas may be able to be cut out and repaired. Such as the back channels can be removed and new metal put in.