Quick update,

I've managed to set the master rail reasonably straight with the setup. It is within +/-5um along the entire length. It was not easy for a few reasons I will outline:
1. The microscope axis is offset in both X+Y from the centre of the carriage, I did this because obviously it has to be offset in Y as you can't 'see through' the carriage but also in X since I couldn't fit the microscope next to the carriage and remain over the frame. This arrangement is highly non-optimal as you are measuring an offset AND an angle. Eventually you get used to how much adjustment to make, however there must be a better arrangement that avoids this coupling.
2. Twisting the carriage hard on the rail can induce a few um of error.
3. Pressing hard on the machine frame and deflect the entire frame a few um.

The conclusion is that with a machine constructed like mine from 80x80x3 box section over a long dimension of 1300mm aligning to an accuracy of +/-5um is probably the absolute limit and it isn't sensible to try to achieve any greater. Also the frame is unlikely to hold this in actual use due to the deflection under force measured. Still it is good to be able to measure these things to get an idea where the limits are.

So in conclusion I've managed to align to ~1/2 a thou with a setup that cost a few quid. It is all entirely dependent on the taut wire actually being straight, however if we assume it is then this setup is equivalent to a DIN 874/00 spec straight edge, one of those 1500mm long will cost £2k then you still have to actually align the rail with it.

Here is a snippet from the alignment:


Quite pleased, time to get the gantry on now!