From my experience with these Bilstein shocks on a 3rd Gen T4R, the 5100s are too tall for the rears and will actually bottom-out on themselves
with a loud crash on big bumps unless you go with their recommended Old Man 2" lift springs,
The Eibach Pro Lift 1" lift springs may be a better alternative. (See link)

With a 2" rear lift in place, the 6112s needs to be adjusted to level ride height. Right?
However, now you will discover that this all changes the geometry of your front end steering.
You now have bump-steer issues because the stock angles have changed.

You can lessen the effect by lowering the front to 4th clip, but it's still there and frame angle is slightly off.
The Eibach 1" lifts can help make better. PRO-LIFT-KIT Springs (Rear Springs Only) - TOYOTA 4Runner Base
My mechanic tells me that adjustable Upper Control Arms (UCA) will fix the Bump-steer problem for around $900.00 installed.

I suggest you go with stock height rear shocks and 6112s struts adjusted to stock height in front.
Verify with Bilstein that this height can be achieved.