If you look close at pic2 you will see that I'm planning to be able to adjust the height and parallelism of the gantry. I think this could be useful in the future if I need to accomodate larger items under the gantry. Do you thing this would have significant impact on rigidity? Maybe I should use 6 bolts instead of 3?
Dave I don't normally quote on system design but I do see a few things here and it also depends on what you want to cut on the machine.
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I would not split the gantry with the two ends as it is very weak as it is already if the budget allows use 20mm end plates and put a couple of box sections across also have you thought about how you would put the bolts in to the bearing blocks and rails etc.
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20mm linear rails are far better than the type you are using and they can be got from China with the screws.
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With a small machine like this and designed correctly I think you would be alright with one central screw. Keep up the good work.