I needa find a way to keep from fillin the airbox up with mud and water.
Seems like from the mud you're riding in, your only other option is some sort of snorkel set-up, either out the hood, or the fender, up the a-pillar, like most. These can be made pretty easily, just using plumbing tubing, and water-tight sealants, theres a lot of build threads for these.
Trust me, I know all about scratches and scrapes, but my cladding was the paint-matched cladding, so it was glossy, and EVERYTHING showed, so I removed it, and Bed Linered my whole Jeep. I'd much rather have the bed liner get scratches, where I can either wipe them away, or just touch it up with more bed liner, than have it scratch the claddings, and I'm stuck with it, and it looks terrible. And all of my wheeling is deep mud and woods/trails, especially during hunting season, and with the stuff I put my Jeep through, I haven't gotten any dents yet. You're just as likely to get a dent in a parking lot, and if it hits hard enough to break the cladding, it's going to dent the doors too. But to each his own, some like the cladding, I hated it, like it so much better without.
But just painting them will make a HUGE difference over the factory look. Even the color contrast alone, the black on that gold-ish color will look much better. And you'll also love the bumper trimmed too, better clearance, and looks nicer IMO.
And the cops are as bad around here with the tinted tails, they got enough to worry about, without having to worry about pulling over kids with tinted tails, haha.