I built this 3-wheel contraption to do this.
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The engine and trans was still mounted to the stub frame when it was rolled out. But I also had removed the fenders and radiator support so there was nothing in the way. I did not have the car lifted very high, just enough to take the front wheels slightly off the ground. I did not put any support under the back end of the car. Only supports were under the rocker panels just in front of the front doors.
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I made no marks or anything in terms of where the stub was positioned before I removed it. There will be shim plates located on the front mounting perches. In my case they were heavily rusted and unusable. For re-assembly, I installed the new stub first:
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What I would have done now at this stage, if I were to do it again, would be to mount the rad support and the fenders to check for vertical alignment or height at the front, and install new shims as needed so that the door to fender gaps are correct. If you have a 2-door car, you might want to check the alignment of the doors. I did. I adjusted my doors so they fit better when closed. I also put shims to move the door hinges on one side outwards (only by 1/16 inch). A lot of times the back end of the doors sag a little and when you close them they are forced up into place. I corrected that on my car.
In terms of the stub frame, the gap between the front edge of the door and the back edge of the fender is what you are working with. For the gap to be even the front of the stub has to be in the right place (vertically), and that's where the shims on the front perches come in. There are shims (or, there can be shims) under the rad support, but the stub has to be first in the right ball park. So in the photo now is the time to adjust the perch shims. I did it after the wheels / suspension / engine was installed, I thought I had the shims set correctly but I had to remove them, it was a pain because of the extra weight and reduced access. You have to err on the side of having the front of the stub on the low side, so that's having more perch shim thicker than you need, but only by 1/32 or 1/16 of an inch. And don't expect that the left and right perches require the same amount of shims - they likely won't.
There's really no side-to-side or left-to-right movement that is possible or adjustable once the stub is bolted (even loosely) to the car.