To start off, I created a mock up of the reactor in Sketchup, a great (and free) CAD/Modeling program. I created the different parts based on images from the movie (the first one) and what other people had done. As it went along I modified things, but the basic design was to cut a main clear ring, 4 stepped sections to support the inner gold rings and slotted ring, and other 'U' sections to mark out the wire wrapping portions.
I planned on cutting all the pieces out, then test fitting. After that, paint would be applied, then everything glued together for a final assembly.
For backlighting I wanted to make a PCB with an array of LEDs that would be behind a white plastic panel, so that light would diffuse. First I lit up a single LED to see how the light would diffuse through the white disk, and got about a 2 cm circle of nice light from about a 5mm space from the disk. So I used that 2cm circle in skectchup around a component of the LED (just a box of the correct width and length) to roughly lay down a layout for the LEDs.
From this I drew out the connections to be made (I decided on 5 rows of 5 LEDs based on this: http://led.linear1.org/led.wiz
Then I drew lines in between all the sections of the PCB so the CNC could separate all the various sections - not the most effective way I know, but I was strapped for time and didn't have the time to figure out how to make a legit one from Eagle
I've attached the Sketchup file for anyone that's interested.
So now I've got all the CNC files I need, time to start fabricating!