The other guy was correct to a point measuring off the tubes. However, when we build ours , the cap is machined so that it fits in the tube tight with a seam left for me to weld. No room for mis alignment.
However, I always stress to my customers to measure off the end cap if at all possible. When our housings are built, they are within .004 of being straight through the center and off the caps so that what makes measuring off the cap better. If the housing is not straight through the middle or off the caps, it doesnt matter how you measure. In other words, when squaring you rear housing, be sure to start with a new or housing that has been checked for straightness.
I also say to square your rear off your front clip and not the bar behind the seat. Most chassis I have found the bar not square with the front. That will not allow you to square the car up correctly.
I also suggest running a little rear steer in the car. This will also help the car on corner entry.
Just my opinion.
Mike
CMG Motorsports.com