I've previously mentioned my sound generators that I've made in reaktor. Another good source of sounds is the good folks over at freesound.org A vast suppository of free sounds and all covered under a creative commons license. Although I've found that the sounds there are a good starting point, and it helps to run them through Cool Edit to cut out noise and trim unwanted bits.
Creating all the sounds at once is a good idea, especially on a project like this which can take several years. Defining a certain group of source samples that you combine to create a certain effect, such as a machine, or a special effect, you can then go and use those same samples every time that shows up in the film, instead of trying to figure out what you did two years ago.
All that's left to do on the film is:
- Color Balancing
- Final Comp