The first step after receiving the boards was to snap off the remaining route tabs and sand off the mouse bite protrusions. In some cases, this is necessary as the boards have only a little clearance around them in the frame. Where not critical, this goes a long way aesthetically. A few minutes with some 220 grit sandpaper is all it takes (note: observe proper precautions for working with fiberglass).
Next, I mounted the SMDs. All of the boards were designed to be easy to assemble with just an iron, but I reflowed the front and right side dev boards to save a little time. For those, I dispensed solder paste onto the pads with a syringe, then placed the components. A few minutes in the fancy toaster oven and they were ready for the next step. Because the right side boards only had one surface mount component each, I didn't bother with reflow and just popped those on with an iron.
After reflow, I inspected all of the joints under the microscope and fixed any shorts or otherwise deficient joints. Next, the boards were cleaned.
Lastly, all of the through hole components and the headers were installed. The final set is shown above; the PCB stack fully assembled is shown below.