Thanks for the feedback. As mentioned above, I am weighing options on my 78 FJ40 resto. I need to either get a new tub and cowl or get new quarter panels, new wheel wells, tub cross member, and patch holes in floorboards. I have a little time left but the body decision point will be here soon.I'd expect to spend some time working the metal to resolve the issues. I've yet to inspect the half doors closely, but I've hit a number of issues with a replacement driver's door. The mirror and lower hinge bolt pattern for the capture nuts is off slightly, which means I'm going to be modifying the hinges and mirror to fit. The door catch area is wrong, so the catch doesn't sit right. The two sides don't align, so I'm going to be massaging the metal back. And the lower lip around the window the metal isn't bent to a true 90, which means the window won't slide in without bending it back somehow to 90.
Nothing insurmountable, but from my experience I wouldn't expect things to be like OEM.