It's details like that lock misalignment that are so easy to overlook when you're doing a complete build of a car. Like you said before, you need to trial fit EVERYTHING. I know you already had them ceracoated but another way to skin the cat would have been to slice it down the middle vertically and weld it back together with a jog in it. I kinda figured you'd bend new parts using some thin stainless sheet.
My new Danchuk door handles had the screw holes drilled at an angle to the door skin so I rejected them. They said the had "no complaints" about them. I got another pair from Trim Parts and the screw holes were correct, but the pushrods were a little short. So I had to put a shim on the door latch to make them work right. It's always something.
Bummer on that magnetic brake coil. I like your idea of the grommet on the lock rod so I'll probably steal it.
The car is looking awesome.