Options for installing linear guide rails ?

[Jonathan]

Ok. I am happy with that for getting the rails parallel to one another

When you're drilling the holes to tap for the rails start with a spot drill the right size to make sure they are in the right place. Could perhaps machine some steel bar with a point on the end and harden it, like a center punch, but the same size as the hole in the rail. Use it to mark then drill the holes one at a time. With an M6 bolt in the hole in a profile rail you get about 0.5mm clearance (from memory) so if it's more than that off you would have to start machining the bolt heads down... bad.

For example, how do most people get the rail level across it's full length making sure there are no high or low spots and ensuring the rail is linear rather than like a piece of spaghetti ?

The simple answer is, I'm pretty sure, that most people (myself included) don't bother. They rely on the aluminium extrusion or steel being flat enough to start with. Aluminium extrusion is much closer than steel but obviously not perfect.
You could scrape the steel surfaces that the rail will mount on (after the frame is bolted down and has 'settled')...that would be ideal but I bet it takes forever. As you mentioned in the first post a taught wire plus optical magnification (with weights to tension and put them in bucket of water / oil to stop them swinging) can act as a straight edge to align from. This enables you to take out any bends is the rail, which there will be, but I'm thinking removing twist is going to harder to achieve?