I'm a little confused on the opening post, talking about how adding long tube headers will reduce boost, so you "must get a smaller pulley". Backpressure does not mean a reduction in power, it's merely a relative measuring system. There was a guy on the ThirdGen boards that had some big-honking turbo in his setup, hit limits, so put on a set of ported aftermarket heads, and even though he was laying down way more power, thought "something must be wrong" because his "boost pressure was way lower".
A few people tried to explain to him that the better flowing heads meant less measurable boost pressure, but he wasn't getting it. Is that the same thing here, or am I missing something?
As for the controls, I would say go with a FAST XFI and TCM setup. That way you can bypass any safeties you want, and let the stock ECM just run the instrument panel.