Thank you for the info. I have been fighting the issue of USB connection loss for a week, so I have not been able to get the rest of z-axis parts cut. I did however get the router mount cut with pre-drilled holes for the linear bearing mounts so they are as perfectly aligned as possible. The M4 x 25mm screws that mount them are slightly larger then the 1/8in. bit I used to pre-drill the holes so I needed to chase them with the appropriate sized drill bit. I was happy that everything lined up on the first try. I am going to try and do the same with the spine so all the rail and lead screw mounts are aligned.
You can see on the left my machine got off track half way through the profile cut.