First off, I didn't bother reading through everyone elses posts. Sorry, just don't have the time right now. I have experience in this area, so take it for what it is worth.
I have a 2001 Mustang GT with the 4r70w transmission. I currently have Mac long tube headers, a mac prochamber w/ mac cats cut and welded in, along with a Mac 2.5in cat back system. Over all, I'm happy with the setup in terms of sound and performance. My only complaint with the Mac exhuast is the h.t.s coating eventually flakes off, and it WILL rust unless if you coat it again, or have some sort of exhuast wrap. Another complaint I have is Mac customer service is crappy, so therefore, I'm finished with Mac simply cause of that last fact.
Following the install of the headers, there was some grinding that had to be done on the shifter linkage to give clearance between it and the drivers side o2 sensor. Not only that, but the Mac headers will not allow for transmission clearance in the event you have to remove the transmission. Least in my case it wouldn't. There are a few companies out there that makes headers for the 4r70w equipped Mustangs such as you will have the ability to drop the transmission without having to remove the passengers side header.
I believe Kooks & Flowtech are the companies that makes them. Not sure about other newer companies like SLP. Probably want to shoot each company up, and ask them before purchasing. Be sure also to get a company that ceramic coats their headers, or some that are made to resist rusting. Just my 2 cents worth.