Source the parts. I used Amazon for perfboard and the LCD, and Adafruit for everything else.
Design the 2D drawings. Inkscape is your friend.
Extrude into 3D. OpenSCAD is your friend-as well as [dnewman]'s Inkscape->OpenSCAD script.
Cut the perfboard to size.
Drill holes in the perfboard and solder the tact switches/analog stick(s).
Thin out the Pi by removing the tall parts (USB jacks, Ethernet, 40 pin header).
Glue on a single USB jack where the Ethernet port was, facing the same way as the HDMI port.
Add a wire off of the 3.5mm jack to output composite video. (Use a multimeter and a known working AV cable to figure out which pin it is.)
Open up the screen and throw out all but the LCD and its driver board.
Find the +5v out from the driver board's onboard regulator. Solder a wire here to bypass the regulator and instead use the +5v from the PowerBoost 500c.