Update! I decided to give Durango Toyota one more chance, since they had a ton of 4Runners in stock. I couldn't tell much about how each one was optioned from their website, so I went in to have a look. I told them I wanted a Trail Premium with KDSS and moonroof. They had three in stock and I could pick any color I wanted as long as it was black.
I asked if they could find another color and they found a red one in Las Cruces. When they crunched the numbers, bringing in the one from Las Cruces would have been $2000 more for an identical truck in a different color. They offered me nearly $4000 off MSRP on one of the black ones, which suddenly became a whole lot more attractive at that price. They also had only the options I wanted and no expensive "fluff" options.
I picked the one with all weather floor/cargo mats and hoped they wouldn't screw me on my trade. They ended up giving me $25,500 for my Wrangler, which was $500 more than I would have taken. They also agreed to swap my new LT255/75/17 Firestone Destination ATs onto the 4Runner and put the crappy Grandtreks on the Jeep.
So I got a great deal on the 4Runner and my trade in the end. The black is going to take a lot of work to keep up, but at least I can squeeze it into my tiny garage to keep it somewhat clean. No mods planned yet, but we'll see...