not as plug and play as some other systems(Holley etc.), but a big custom one is called Megasquirt-this is the website I looked at-was thinking for an aircooled VW at one point.
http://www.diyautotune.com/
another thing to think about is ignition, major improvements can be made by improving spark curves, MSD or even Megasquirt again.
I think Megasquirt is best for custom applications like this, but I think I'm biased, I like to know how things work and how it goes together, so if anything happens I know where to look
doh! didn't see initial post, too long of a day apparently