Morning Magnon, about your removal of the hinge plate, making locator holes seems like the best idea, if you don't end up replacing metal in the process. In addition to making the locator holes, I would take measurements from know position on the inner door structure.(ie top measurement from top hinge plate and inner structure to a known point on the hinge plate you are removing, doing this assures you if there is an "OOOPS" somewhere you are swearing at yourself.
This is what I did on my 67 that I am resurrecting, this thing is FULL of rust and I have replaced copies panels and structure.