I think you need to get your head around moving things around. The move tool will rotate groups around their center and snap to axis. So you can easily make things 90 to each other.
Endpoints and hidden geometry makes it easy to grab things in the right place so you can align them.
The arrow keys lock to axis.
So here I have rotated the odd pipe to match the vertical pipe, then move it into place with a middle vertex to another middle, then move it along the green axis to center by aligning the two midpoints on that side.
