After thinking about this a lot and getting all the great input from everybody here, i think that on my budget with my resources and skills, the project is not feasible for me. I am not saying the project is impossible, but somebody in my position probably would not be able to pull it off.
The reasons I believe this is as follows:
1. My budget includes both the computer components, as well as the necessary cooling equipment and whatever I will need to create the case. Currently i budgeted about $1,000 to the computer and $200 for the case. I don't believe this project will stay within budget if I am going to be buying extra components like wireless USB hubs, fashioning aluminum saucers with supports and fiberglass struts and using copper piping.
2. I don't believe I am skilled enough to even create a saucer out of AL, and my painting skills aren't good enough to actually finish the ship off. I was willing to attempt it, but with so many other shortcoming in the project, it is just another nail in the coffin.
3. A lot of the problems we have been discussing throughout this thread are substantial problems that can be overcome, but that are just not worth it in terms of time and money spent to get it to work right.
4. The computer will be at risk of overheating due to poor ventilation in the saucer, thus not allowing me to overclock.
5. Many of the workaround to the problems are basically taking the computer out of the ship, which defeats the purpose of the project.
6. Many workaround still do not meet the goals I set out to achieve.
Through all this, we have all learned a great deal, but after all this, I think this project will not happen. The purpose of this thread was to determine if this project was doable. I think what we have learned is that yes, it can be done, but it requires a great deal of effort, time, skill, and money. I only have one of those four things in abundance, maybe a bit of skill too, but in general, I am not cut out for this project. If anybody else is willing and able to do this, by all means go for it, as I would love to see this happen. Unfortunately, I am in no position to be the one to make it happen.