Yes you have to cut the tube. With the aluminum tub you dont need the alignment tube and it actually gets in the way on the aluminum tub so u have to cut it. Here is my build thread: Builds - Fj40 Daily and Wheeler buildOk. From what I can figure, I'm going to have to cut the tube for the top down the middle in order for it to line-up. Right now, the tube is all the way against the aluminum tub vertical channel and can't be moved outward. How did you rectify that?
My cruiser is a bit more of a offroad build but most the details of my tub install should apply to you. As I mentioned, as you line things up clamp it with c clamps. Once all parts are mocked and lined up you drill your mounting holes.