Sounds like you're doing the same thing I am. Which sound card are you using? One of RMEs? Lynx? I'm not sure I'm aware of one with hardware equalizers?
What software are you planning to use with the card?
I'd put the computer in the back. If your going to all the trouble to eliminate interference, why not just have a short ~1 foot RCA run from the sound card to the amps? A 10 watt CPU shouldn't have any trouble in the trunk without the benefit of an AC connect (plus AC can result in condesation, and thats a no no).
You can always put a 2nd battery in the back if that concerns you.