Cut the threaded rods to size with the hacksaw. Stack the boards on the rods, reversing the orientation of every second board so that it is upside down with the ethernet jack facing the opposite side of the stack; this will result in ethernet and power jacks down two opposite sides of the stack, with serial ports on another side and no connectors on the remaining side (which is the "bottom" of the stack). Use the 1.25" spacers between adjacent boards in a right-side-up/upside-down pair, and the 0.25" spacers between pairs. The grounding strips on the top of each ethernet/USB connector tower will just touch the plastic cases of the LED drive transistors on the adjacent board in each pair. Fasten the stack with the acorn nuts.
Gather the barrel connectors in groups of five. Connect each group to the +5 volt (pin 1) and ground (pin 2/3) leads of a molex connector from the ATX power supply (cutting off the cable connected to the molex connector, and ensuring that the barrel connectors are wired center-positive). Solder, then insulate with shrink-wrap tubing. Take the motherboard connector of the power supply, pull off all of the leads except pins 8 (PWR_OK) and 16 (PS_ON), solder those leads together, and insulate with shrink-wrap tubing. Plug the molex and motherboard connectors into the ATX supply.
Place the stack on its side on a wire shelf for convection cooling. Test the power supply leads to ensure you're getting a solid +5 volts, burn and insert your SD cards, connect your ethernet cables, and connect the boards one at a time to the power supply unit with the barrel connectors.