On a four door Explorer, you can just cut off the rocker panel. There's no interior access (like on the Sports), so it's fine to cut it and leave it.
You can also cut it and weld in a piece of rectangular tube (1/8" thick 2x4" works great, but you can go thinner if you just want it for cosmetics and can find it.
Most expensive option is to buy new rocker panels and have them welded in, not to mention the cutting and bodywork involved as shown in the thread.
But you might also be able to just cut out the existing rust and have patch panels welded in place rather than replace the entire rocker, though if it's rusted, it's best to replace EVERYTHING ...AND get rid of the tupperware, since the holes the retainers use in the rocker is what lets water and salt in there and rusts it out to begin with.
As for the exhaust, the stock converter is fine. There's no point in an aftermarket one unless the factory converter is clogged up or something. They are $200-300 new, which is hella expensive for something just to have a shiny one. The Dynomax catback works fantastic with the stock manifolds and converters. The only thing I'd suggest is a KKM True-rev kit, or at least a drop-in K&N filter. Keep the MAF sensor and throttle body clean and it should be more tourquey than ever. Don't forget the throttle cable 'mod' for proper tension on the gas pedal, too.
Sad to hear about the mustang, but your X should serve you well.
