Are you sure that door hinge alignment tool is the correct distance between the hinges ? Check it against the actual door.
Also, it looks like the tool is fitted upside down, the angles of the parts which replicate the hinges look wrong.
I would fasten the front bulkhead to the heater channel, either by welding or temporarily with 'L' brackets and TEK screws.
Do not lift the body by the door gap brace, I think this may be warping the bodyshell, instead, use a pole to lift at the top of the door opening/roofline.