Cut, drilled and installed shims under the gantry plate. Also reversed the 2 upper mounting screws on the y-axis stepper. Altogether that gives roughly 110mm of motion. I will have to drill out some of the holes a bit wider and possibly straighten the rails because currently there is some binding in the Y-direction motion.
Installed gantry plate successfully, but apparently there is insufficient clearance with the ballscrew support blocks for more than 1 inch of motion in the Y-direction. I will need an additional 2mm shim on all carriages and possible 3mm on the ballscrew follower nut. 
Cut, filed, drilled, and deburred 4x linear rail carriage mount spacers for the y-axis motion system. Ordered the corresponding length screws to mount the gantry plate.
Bolted down Y-axis ballscrew supports, installed lubrication nipples, vacuumed the entire assembly, and lubricated the rails and screw. 
Installed ballscrew nut follower onto Y ballscrew. Determined height of linear rail carriage spacers (25mm ~ 1in) and ordered some aluminum stock for that purpose. Also printed templates for the clearance hole patterns. To simplify this process going forward, I spent some time configuring my network printers.
Cut, filed, and drilled clearance holes in some spacers for the ball screw support blocks for the XY gantry motion. Took a while to saw because my hacksaw blade is getting quite dull. Used Inkscape, my printer, and a gluestick for the first time in this application to actually mark out the drill locations, which worked swimmingly. I do need longer M5 bolts to mount these, however. 
Trimmed roughly a quarter inch off the end of the ballscrew to make the entire Y-axis motion assembly fit in the frame interior (barely). Installed the stepper motor bracket in the proper location and then installed the stepper itself. Determined that 18mm of shimming will be required below the ballscrew support blocks. I have various aluminum stock thicknesses that together stack up to that value, and I can cut and drill those this week. 
Calculated, measured, marked out, drilled and tapped holes for the Y-axis motion control on the X gantry plate. Installed the linear rails. Because space is tighter than I anticipated, I'll need to saw off a bit from the ballscrew and possibly even some from the drive shaft on the stepper. Not ideal but it should work. I'll also need a different stack of spacers between the ballscrew follower thingamajig and the XY gantry plate since the stepper mount is different, again since space is so tight. 
Put final counterbores into X-Y gantry plate and test-fit the linear rails and ballscrew ball nut carriage block. Somehow miraculously everything is aligned. I do still need to put in tapped M5 mounting holes for attaching things. 
Began to drill and counterbore mounting holes for the X-Y gantry plate. These slotting counterbore bits are really nice but get gummed up quickly and stall the motor of my weak drill press. Also have to use a cordless drill to reach the central holes. Would be nice to make a nice drill press. 
Took inventory of CNC mill project after long hiatus. Updated CAD model to reflect length of installed collet and bit and migrated to organization repository. Marked out the drill and tap locations for the X-Y gantry plate. 
