Definitely get the trans tune too. I drove 1500 miles with stock tune and was very happy but with the pcm and trans tune it's like having a new Jeep. GDE has great support too.
I used brand x and MC geo correction brackets and I found the design of the MC are better because of a sheer condition I had with brand x. The MC brackets are staggered to mount in the factory mounts where the other brand was sandwiched in the factory mounts. Think of twisting the geo bracket...
I just did the GDE & trans tune and the jscan does work to update the tire size. I am on 37" and stock gearing. This is the best Jeep of the 3 I owned.
Congrats on your JT and welcome to the forum. Take a look at the others build pics to help you decide how much lift and the limits for each. Best part of the JT is that you don't have to rebuild or engineer new parts to get a capable 4x.