I would do some "shakedown" trips if you haven't already. These will tell you what you need, don't need and are nice to have. I think the biggest thing on long road trips is to get and stay organized. You can do this with plastic bins or you could build a storage platform. Some platforms just get you organized and some also can be slept on.
http://www.toyota-4runner.org/3rd-gen-t4rs/81843-rear-cargo-box-thread.html
Pre-trip maintenance is a big one. If you think it should be done then you should do it.
I would consider some type of rooftop storage. Hard cases (bins or top carriers) are easier to stay organized and some are more aerodynamic. Soft roof bags work fine and keep things dry, weigh less and cost less. I would use the roof for chairs and stuff.
You could consider a hitch type carrier. This keeps stuff out of the wind and is easier to access. But it will hinder getting into the hatch and will drag on wheeling obstacles. I would use some type of plastic bins on this.
----------------------
I would recommend, if wheeling alone, some type of winch. (Come-a-long etc)
If you want to do some harder trails, hook up with some locals so you don't wheel alone.
I would definitely have a CB radio to talk to locals when wheeling with them. Also great to find out why traffic is stopped on the highway. Ham? your choice. I know of a few wheelers that use them.
Window screens?
The Skeeter Beater - Magnetic Screen for your car, truck, SUV or RV. They work well.
High altitude clothing. YES! It does snow all year long at altitude. Be prepared. The mountains can get rain in the afternoons. Colorado is #2 on lighting strikes too. You may want to think about some type of tarp/awning for camp.