Refasten the lid onto the power supply. Screw it back in place, gently refasten the motherboard to the power supply and RAID card and then screw it back down on its posts. Don't refasten the bottom of the case yet.
I don't know that you really need it, but I feel better being able to exhaust air from the power supply. So I placed a fan on the new top of the case and marked the corners. Then I spent a few minutes drilling holes in the top of the case – four large ones for the fan mounts, and many more as an "exhaust grille". I mounted the fan just behind the front feet on the case, so it's directly over the heatsink.
The Silenx fans come with very nice silicone fan mounts. You don't need them, but they're easy to use up top. After you've drilled your mount points, tug the fan mounts through from the inside and you can easily fasten your top fan.
I threaded the power up through the ventilation slots to avoid fouling the fan. The trick for taking the leads out of a power connector comes in handy here, too. You can free the fan leads, carefully keeping the leads separated, and apply power to the unit. Power it on and figure out which ones are which. Power down, and you can either solder or slip the fan leads back into their sleeve with the power leads tightly wrapped.
Fit the second fan to the back panel, confirm that it is also seeing power, and you're ready to button up. One thing which I've found makes a significant difference: in my mod, I'm exhausing heat out of the top, so I want to use the rear fan as an intake fan. When I used both as exhaust fans, the drives and CPU warmed up significantly.
Most of the case screws are going into plastic fittings, so don't overtighten. Find yourself a few rubber feet for the new botttom of your case if you like.
Figure 5: Reassembled case with external "power supply" fan
I've fitted variable speed fans to both the top and rear since I started, and modified the rear grille to thread out a cable for the speed regulator that you can see in Figure 5. I am finding that the Antec 80mm fans are quiet, but are either not true to speed or not accurately reporting speed. This is annoying because I have a warning in the system logs and an amber light on the front panel that is staying lit. I have to run that rear fan flat out to clear the light, and so I'm still looking for a perfect 80mm fan.