Step 3: Cutting the NES to accomodate
There are several modifications you will need to make to the NES case internally to fit the Wii main board and DVD drive:
Start with the bottom half of the NES case. I used a 5/16" drill bit to drill down all the screw holes OTHER THAN the ones that hook the bottom half to the top half and the ones for the Power/Reset switch (a Dremel tool/cutter would have been more efficient, but there wasn't one available at the time I did this project).
Remove the bottom cover, and cut out the expansion slot plate (y'know, if you wern't like me and didn't do it 20 or so years ago). From here, you need to sand down so everything is fairly even with the raised up sections (again, except where the power/reset switches are).
At this point, you should be able to take the more flat portion of the Wii case (picture #2 below) and set it inside the NES, and it will lay flat.
Now, we need to make sure we can put the expansion slot cover back on:
Place the flat section of the Wii case on the bottom of the NES with the screw holes up, the controller ports facing the back end of the NES, and the place the battery goes toward the front.
NOTE: In the picture below, it's showing the Wii case as far back and to the left as possible. This is incorrect (as I found out later on)! To see how much room you will need, place the Wii motherboard on this plastic piece, attach the DVD drive flexible flat and power cables, put the top of the NES on, and verify both cables reach where the DVD drive will go (about the center of the NES flap).
Orient the Wii case as far back as it can go (level with the A/V and power port holes) and about 3/4" from the left side (assuming the power/reset switch holes are away from you). While holding the Wii case in place, flip over the NES and draw a mark around where the expansion cover clips in. Using your drill or Dremel, cut out these small rectangles. Now (if all went well) you should be able to place the expansion slot cover back onto the NES and have it clip to the inside of the Wii case.