After a bit more thought and a little more reading on the subject, i I think that using copper for the hotside piping and aluminum/steel for the coldside would be the best way to go since it could help shed a few degrees before it even reaches the intercooler.

Ok I found the article I read long ago that first sparked my interest in using charge pipes as a means of aiding the turbo, and it is written by Corky Bell, and while he is not using copper, it really illiustrates how important it can be.

http://www.bellengineering.net/Pages/comments.html
go 1/3 down and look for the headline: Intercooling & Interesting Twists