I was thinking about this today instead of studying for finals, and I came up with a couple points.
1. If you're talking about a header like this (
http://cgi.ebay.com/ebaymotors...38148), you're going to have trouble finding a place to put an external wastegate. There is no real collector area on that thing... it seems like you're either gonna have to wastegate a single runner (ehhhhhhh) or use an internal wastegated turbo.
2. If you're just gonna cut the flange off, there is no need to limit yourself to only SR turbo manifolds. As long as it fits in the space that's there in the engine bay and has at least semi-similar runner spacing (I dont think they could be THAT far off if its another I4), any manifold would work.
Just some things to think about