Alright, well I figured out how to get my router rounding bit to round correctly. I had to do what sy said, and I had to change it to the 1/8" bit for my 1/4" acrylic.
After rounding the Motherboard piece and lower piece, I sanded the edges a bit and went over the edges with the budding wheel. I then glued the lower PSU/HD/DVD drive area to the Motherboard piece.
In order to finish these two pieces I still need to cut all of the small pieces which will hold the HD's, DVD Drive, and PSU in place. I then need to cut the wire routing holes on the top piece, drill the holes for the motherboard standoffs, and cut the piece that will go behind the PSU to hide some of the wiring.
Here are some colored images of the design.. (it will all be clear though)
