You can run a 4.5" MAS adaptor with the MAS in the stock location. Just have to get a 4.5-3" reducer. Thats how i ran mine

If you want to use the pipe from the MAS -> Throttle body you have to cut one of those pieces. You more then likely will have to cut one of the pieces for the CAI extension to work anyway.

For the MAS -> Throttle body just cut one of the bends off one of the pipes(the one with the nipple) and just use a 4.5-3" reducer on the back of the MAS to fit to the pipe. The 4.5-3" reducer fits on the back of the MAS just fine.