That is correct, I only paid tax on the sales difference.
In all honesty, this has been a hellacious journey to the 4Runner. In March 2015, I bought a Power Wagon Laramie. All told, it spent almost 8 months in the shop between November 2015 and October 2016 due to death wobble, leaking rear glass, and a leaking brake light. After lawyering up, FCA and I finally came to an understanding and they bought the Power Wagon back. In exchange, I had to purchase another FCA vehicle. Wranglers are pretty much the only ones that hold their value so I ordered a JKUR Hard Rock.
I ended up losing about $3k on the Power Wagon -> Wrangler deal and another $3k on the Wrangler -> TRD Pro deal. It could have been much, much worse and I'm just happy that this journey has come to an end. On the bright side, I've owned 3 brand new vehicles in a little over 2 years....which will probably never happen again in my lifetime.