Cheers Clive, good method.

Had a go at sorting out the beams today. I set the front beam using the datums I'd left on the bed:
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I used some shims to take out the slight rocking on the underside and get a better clamp:
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I then started to skim the face of one of the beams taking off as little as possible. I'd hoped this would only need to remove the high spots but in the end I had to machine back the entire face to get back to a level surface everywhere. Probably had a slight twist in it.
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Looked good. Actually this is the first bit of steel I've machined on this CNC and I did get covered in tiny showers of swarf. As it is hot today I had a T-shirt on and they were very hot!

Anyway, then I offered it up to the gantry and as I tightened the bolts I watched for any movement - there was none. I tightened all of the bolts then tried to rock the assembly and unlike before it was solid, there was no rocking on the base plates which means success! Very happy and back on track. Hopefully the other beam is just as straightforward.

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Looks quite nice although the steel bits will all get painted.