Bob
You machine every thing true,machine evrything nice and flat, bolt it all together, and that is how it comes out. In my opinion, based on my experience with my Rail Gun, it does not have to be, and probably will not be, dead nuts true.
As for the tracking, that is determined by how true you actual rails are with each other. That is why it is a good idea to have one rail adjustable, you can play with it untill it tracks dead on. By tracking dead on, I mean when you look through the scope and slide the top back and forth, the cross hairs do not move off of POA.
But even that is not nessessary as long as you put the top back against the stop each time, and the cross hairs come back to the same POA.. With different weight barrels, mine will change, because the weight actually flexes the top down just enough to make it track off up and down just a little.
But, honestly, I quit paying attention to that sort of stuff, because it just does not matter.
Well, let me qualify that. If someone happens to walk up to you Rail Gun while it is sitting on the Bench, and moves the top back while looking through the scope, and it does track dead on, you will get a big "attaboy", and you can pontificate about the hours you spent getting it that way.
Aside from that, it doesn't matter........jackie