One of the new steel bolts will penetrate the tray.

After bolting the heatsink to the northbridge chip, fit the PCB over the tray, and push gently down on the metal bolt that makes contact with the tray. It will leave a mark on the tray. Drill a 5 mm hole at that point.

From here on the reassembly process is the reverse of the disassembly. I have not photographed each step of the reassembly, which is pretty straightforward. Before returning the CPU tray, clean out the interior of the Mac Pro case. Use compressed air to blow out dust in the fans.