I agree that this is a significant project without a lot of knowledge and research. Although this would be a good learning experience, and probably fun, it could very easily turn into a big waste of time and money without being able to make something worthwhile the first (or second..) time around.

If it's just a D16, why not try to optimize the stock plenum through extrude honing and port matching? Unless you're running some serious flow, or have some reason that the stock plenum won't work, it's going to be hard to improve upon the stock piece for what you're doing. For the power gains you're talking about, this might be time (and money) better spent elsewhere. You'd be amazed at what an extrude honing can do for flow, both volume and quality.
This all goes out the window if you're talking about an ITB setup obviously. My advice if you're going that route is to start with a new flange and build from there, the stock casting can be used with coupler-type ITBs but it's not that ideal and usually ends up a bit ghetto. Starting with thinwall straight tubing for the runners will give better results..