The door you got was more than likely fine. The doors size makes it unable to square until installation. If you stand the door up on a level surface and then square it by nailing triangular plywood gussets on the face of the frame it will hold square. The thin frame jambs will also be bowed and out of plumb from the factory at times. This is why we always preach that the installation of doors and windows is the most important piece of the puzzle. The standard homeowner or DIY person would not know that the frame should be squared during the installation process and not off the truck.

The installation of the door requires a nice flat and level sill. If it's out of level then level it out with plywood. If it's just a bit out of level, you can bring that correct with shims after you insert the new door. Make sure you put a good healthy bead of silicone under the new frame to seal the bottom. We usually put down three lines to seal the bottom. Ounce you get the bottom sealed and level the frame can be shimmed square at that time. If you can't get it right just get it close because you can adjust the rollers on the bottom of the door to make the reveal straight. So don't ever expect any door frame to be square upon arrival. It was built square but shipping and handling knocks them out every time. It's the installers job to square it during the installation.

Guy exterior man, you were right. I found the reason the door frame was not square was the bottom of the frame that includes the track was bent downwards in the middle. I set the middle of the door on a stack of newspapers so most of the weight was supported in the middle and let it sit in the sun for a few hours. Gradually the bottom of the frame straightened out and now I only had a 3/8 inch difference in the diagonal measurements instead of 1 1/8 inch like I had before. I don't think I could get it any better as the fixed panel was slightly out of square and there in nothing I could do about that. But anyway I figured this was close enough and went ahead and installed the door. It took two days because the sill was not level and I had to wait for the stuff I used to level it with to dry overnight. I still have to trim the interior.
I only wish Certainteed would allow you the option of getting the door delivered wothout the fixed panel mounted in the frame like Superior allows. That frame and fixed panel are heavy and cumberson to move. Took me, my wife, and two of my daughters to move the thing.
The job turned out pretty good if I say so myself.
BTW, the window companies all say that their two man crew can remove the old door and install the new one in three or four hours. I don't believe they can do as good a job as I did in that short a time. They probably slap it in there and hide all the problems with trim.

Californian, I'm glad you got it figured out and were able to install it. As for time of installation for two experienced installers, three to four hours is right on the money. My son & I do them in about three hours depending on the problems we may find. Usually if the floor is out of level we have to tear out the old wood decking and replace it, or use Pour Rock on a cement floor. Either way adds anywhere from an hour to three hours depending on the work that has to be done to bring the opening up to satisfaction. As long as the new door is ordered correctly to fit the opening they are generally pretty easy. The weight of the doors varies from door to door. We usually pull the active glass panel out and carry it up separately with only one man. The inactive sash and frame is also usually carried by one man unless there are stairs or difficult maneuvering to get to the opening, but we are also a bunch of brutes also. The Andersen patio door comes in pieces, which makes it the easiest door to move. The frame comes knock down and has to be assembled on sight. The door panels are separate and carry up pretty easily.

Hope it all works out when your done. Good Luck!!!