I put a Magnaflow system on my '66 GS. Amazon had them on sale a few times for under $350.
It's a header-back system, but it comes with 3 tailpipe outlets so there was enough pipe left over to attach it to the stock manifolds. I used the original flanges with the ID opened to 2.5", and hand-formed the flare to mate with the manifolds.
I know I put a few pics up at V8Buick, but don't recall if I posted them here also.