Can you get a measurement off the door opening using a right angle...framing square, or one of those cool new digital levels that gives a readout of the angle, to see if both the openings are the same say from the rear of the opening and bottom sill?
Somewhere you have to establish a level baseline. (can't remember what these look like) I'd try to get it up on jack stands with the frame bubble level. Then proceed from there. If the body is supposed to sit level on the frame (likely), is it?..Then move on to the door sill at the rocker panel. Is it supposed to be level? (perhaps, but maybe not) But is it equal to the other one? Once the frame is level you can, for instance, clamp a piece of steel under the car and use it to make accurate vertical measurements from (can't trust the garage floor) If the garage floor is off by say 1/8 inch it will really mess with your efforts to find the problem and correct it. The plan here is to make a shade tree frame jig. Then you can see with confidence where things are out of level and what is needed to correct it. Probably would be a good idea to do something to replace the missing floor brace as well. It's likely you can get replacements for those.. "Chevs of the Fourties" I think is the name... Someone please correct me on that. Patricks perhaps. There surely is someone who sells them. Or fab one up.

Sincerely:
Paul...aka xerxes