DXFs of the Cupcake CNC y-stage and z platform modified for cutting on a CNC router with a 3mm bit. Slots have been resized for 5.2mm plywood.

A couple of notes:

1) Holes for the magnets are round, but should still be a tight fit on the corners of the magnets. I don't think this will be enough, so I'd recommend using epoxy glue or something similar to fill the gaps.
2) Like the x-rib, instead of a series of slots for timing belt engagement the y-rib has a recess for permanently gluing a short length of timing belt. I've included a STL file for this part - if anyone thinks of a better way of doing this, please let me know.
3) some of these parts are small and delicate, so take care while cutting. I haven't tried it yet, but I will as soon as I have the chance.

Related things:
Routerized Cupcake body panels: thingiverse.com/thing:1864
Routerized Cupcake X stage: http://www.thingiverse.com/thing:1881

1) Cut on CNC router with 3mm bit
2) Glue in section of 6mm G2 timing belt
3) Assemble.