First: Do you weld or fab in your spare time? This prject WILL take custom work, especially for the v6. I would call reputable fabrication shops around your state and see about costs for making a manifold and downpipe. Charge piping will have to be done by someone as well if you
do not have any friends / connections.
Also for management, several options exhist, but the two I would look at is the Greddy Emanage Ultimate?? or Megasquirt.
On the trans side, you sure it will be more conomical to swap in a manual, or would it be easier to get the auto built. Tony seemed to keep up with that vette pretty well
EDIT: One thing a bud did on his sc400 was hire a draft/design undergrad to design a manifold, and he had it fabed from his designs. It was badass B) to say the least. Just thought Id throw that in for ya.