Oh hey Doug. I was about to run through some emails later this evening and reply to you. I'll still do that so let's just stick to this issue.
I am not certain if you have a regular back that fits smoothly. If I had what I see on your photos, and I was confident that the back is sitting tight into the camera, I would bend each tube on the camera body until the hinge pins on the back settled into place. Crude, maybe, but this camera is a Chevy pickup, not a Rolex watch. If you take a small block of wood the width of the tube, place it against the side, and give a tap with a hammer, it will move the tube slightly. I'll leave it to you to figure out the direction needed.
I would do one tube at a time, check, and see if the second pin on that side now works better. And check the other side at each point in case it too decides to now fit.
And before someone jumps on me (yeah, looking at you, John

I've worked on maybe 100 Medalists and run into most any problem possible. This is one, and this is how I fix it. And banging the tubes works! If that bother you, two other options. Protective jaws on pliers to bend the tube. Or put a metal rod like a screwdriver in the tube and bend it. Common thread here- bend. Two reasons to focus on the tube on the body- 1, it is held in place by screws, attached to the cast body, and can be replaced if something goes bad (basic criteria for taking a hammer to a camera!). 2, unlike the tubes, the part on the back is riveted and attached to an aluminum sheet metal assembly that could be distorted in hammering (another fix for backs not fitting: spread the sides out a bit by pulling on the back; now this is a tricky one to describe and if you haven't bent metal by hand before probably best not done).
As to focus: No, the ground glass in the accessory back is not in the same position as the film plane with the regular back. But here I'll bug Doug in email and stop.