Re: Rear clip alignment
Body fit is one of the trickiest parts of a build, especially from scratch. I tried to first center the wheel well arches over the tires then establish the rocker panels from that. The bottom of the rocker panels should be at the bottom of the car. Essentially the rocker is centered between the tires and aligned with the bottom of the car. Then all the other parts are aligned to the rocker panels.
My rear clip wasn't trimmed on the front edge so that made it even more problematic. That trim made it possible to tilt the rear clip to align it with the rocker panel.
The rear bottom edge of my rear clip is 4-1/4" from the bottom of the car. The original cars have a nice curved assembly of aluminum sheet/steel tubing that goes from the bottom of the car to the clip rear bottom edge. You can see it in the parts book.
Another thing you have to keep in mind is these bodies aren't symmetrical. I spent a lot of time trying to get the clearance the same all around the back tires and it just wasn't possible because the fender curve is different side to side.
One other note, the front clip bottom is flush with the bottom of the car.