Yep, you're spot on. What I would do iffen I were you - is to build your upright supports, but don't weld them to your jig just yet (more on this later). Attach them to the specified points on the frame rails and lower the car onto the body of the jig. The car will most likely settle into this position and once you double check your measurements, weld the uprights to the jig. What I think is happening is your car has sprung because it's only being supported in the middle. It's not serious as you see this everytime you lift a car up by the k frame. As you jack a car up, watch the gaps between the door and fender and the hood and cowl. They close up before the wheels even budge. Unibodies are like spaghetti, they bend pretty far before you do any damage.
Right now, your car is not in a natural state. It's not supported like the frame chart would have it and it's not sitting on it's wheels so all bets are off as to whether or not it's tweaked.
My uprights are square tubing with a piece of angle iron on the top. This mount (angle iron) has a 1" hole in it for attaching the frame rail. I made 5/8" T bolts to fit into the existing factory holes so the car can be easily mounted and dismounted. If you weld the uprights first, you must be spot on as to the location of the holes in the frame rails and as we all know, Ma Mopar wasn't always terribly consistent. Just because they should be, don't mean they are.
This is the reason you bolt the uprights to the car, lower it into position and then weld them home. It may take a little while for the car to settle into position, but if it is indeed off by an inch, it'll show up here. I hope this is clear - it's easy to grasp when you see it, but tough to 'splain.