Thanks for the advice Jazz. OTT... please see observation below:-)

The granite slab I welded on is pretty flat and judging from that the two areas where the 2 X base plates will be welded is very much on the same plane, so no significant twist. I would say definitely less than 0.5 mm which is great as I was prepared to deal with 2 or 3mm if I had to. My plan is to weld in the 10mm base plates and then let the gantry settle under its own weight on top of the two alu blocks that sit on the linear guides with metal epoxy in between and release agent on the alu blocks. That way I should get a very good mating surface there and not induce stress bolting it together.

Two observations that might help other newbies.
1) Parts looks a lot more bulky in real life than on your little cad drawing. If you go with 'looks about right' on your cad, it will translate to 'way over designed' in real life.

2) Holding the parts for welding with threaded rod works well but put washer and maybe copper slip on the nuts as they may bind due to movement during welding which makes them hard to remove. I had to cut one rod to release the longitudinal stress that caused two nut to lock up completely.

3) Early in the weld a thin tag weld broke in half with a very loud ping sound during cooling, and I thought this is the beginning of the end as the offset on the broken tag was quite obvious. I did the opposing welds and when that cooled the tag had moved back to almost its original position and you could barely see the hairline crack where it broke.