I used mastercam for the cad and the cam.
The logo I modified from the standard one. All the curves are arcs, not segmented splines. I sketched most of it, then cut vertically down the middle of the logo, deleted the remaining unwanted half, then mirrored the half to create the full logo. This insured the logo to be truly uniform, and eliminated most of the dimensioning.
I'm not really clear on what your asking about keeping things lined up. When flipped on the cutting table to cut the reverse side, the screw holes lined everything up. After buffing, the holes are countersunk. This removes any defects caused by the hole during buffing.
I modeled the piece from the original by using a good set of calipers to measure the features on the old part.
Eagle One has some great stuff call nano-polish.
I've used it on parts that are now 2 years old, and they still look good with no corrosion. My only complaint with the wadding type polish is that it gives everything a chrome look, instead of a polished aluminum look. It does do a superb job, though.