I was looking at the setup sheets and saw something about flipping the top engine mounts over to move the engine back 2mm. With this small move rather than the 8mm move do you still have to relocate the center diff? and do the optional center shafts need to be used?

No, mid to front diff location stock bones, mid to rear option.

I wrote to put the diff in the middle, that's how I ran it.

There are 4 locations for engine and the diff slides the whole 8mm