Both of these questions are best answered in-person, with a local offroading club. Nothing against Jeeps, but their trucks don't have our technology, so you'll want to talk to mostly experienced newer Toyota owners who know how your truck works and can tell you what technology to use, and when to use it.
Here's a local (to you) Facebook club to connect with:
https://www.facebook.com/groups/901624000018385/about/
And here's our club in Colorado, one of the largest / most active in the country if you ever want to come up north and run with us:
https://www.facebook.com/groups/ColoradoFJCruisers/
My advice: figure out a goal for your truck. What do you want to do in the outdoors, and then how do you build your truck to do it? Are you a camper? Fisherman? Technical offroader? And then talk to your club about doing these things, who else does them, what equipment they selected for doing those things and why.
Example: rooftop tents are great for camping, less so for super technical offroading (they scrape on trees and add a lot of weight up high). What armor you choose (if any) is a factor of how hard you want to offroad. Tires, same thing. Your goal is to define an end destination for your truck before doing a lot, that way you don't have to do anything twice.
Remember this saying: it's always cheaper to do it right than it is to do it twice.
You need a vision for what you want the truck to do, and the experience doing those things to make these ^^^ decisions. You'll get that from spending time with other FJ / 4Runner owners in your area, seeing what they do, how they do it etc.
Also FYI, your location -- Farmington NM -- is very close to the annual location of FJ Summit, in Ouray CO. You are a very short distance from one of the best FJ playgrounds in the country. So there's no shortage of great offroading near you.
