Sounds like it will be a BEAST when you get it sorted out!
Mine had idle issues after the headers got installed, but a quick adjustment to the tune cured it. I have a local tuner that is great!! I think you are going the correct route with a local guy as long as he knows what he is doing!!
I'd like to hear more about the SW headers. When I was in the market for headers, it was between SW and American Racing. I couldn't get SW to give me a single reference of a customer for my model year (04-08). The only truck was their demo. and wanted more of a testimony than the "salesman's". Needless to say, I went with American Racing and couldn't be happier.
Good luck and keep us posted!