Depending on availability, and the space you have... you could always try to find an old rear A/C unit in a junkyard... many conversion vans have these... but unfourtunately I can assume many get picked up quickly or have many leaks... but its worth a try. Of course if you have too much money to know what's good for yah, you could probably get one from a dealer. Just a suggestion since running a tube seems to be hard. The only problem I see with the fans under the backseat to the trunk is the back of the car usually doesn't get cool enough quick enough, or at all if your A/C really sucks...lol
I'm sure someone out there has a good idea on how to do it... I'm actually really interested in the idea now even though I drive an SUV and dont have a trunk. It could be useful no matter where the computer is just to make sure you don't have any skipping problems... a cool computer is a happy computer!