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Create a 5cm high bumber corner that the blocks can be clamped onto.
I would carve the bumper with the corner as XY0 so I know the reference point match that of the block.
Insert block 1, zero Z, carve, take out 1 and insert 2, repeat
I was doing something similar for some chess boards I was making. I took a scrap piece of pine and hollowed out 6 squares (using dogbone corners) the exact size of the blocks I was cutting on. This also levels out all the blocks so they are the same height. Using the same .crv file, I then put the design I wanted to cut into the center of the square so I knew everything would be lined up. I ran into some issues with the blocks having a little wiggle to them so ended up using the masking tape/CA glue method of holding down.
I really like the solution that was done in the video Haldor posted and would probably modify what I did to use clamps that were marked so I could cut more than 1 at a time. Those straight line clamps good pretty good, too.