Yes, you'll need custom programming for the long tube headers. This is not to "take advantage" but to insure the check engine light doesn't come on and the computer goes into open loop operation due to a false O2 reading.
Superchips no longer provides custom tunes. They've discontinued all of it for chips.
The 4 digit computer code can be found on the computer box where the wiring harness is bolted to it (firewall, driver's side).
I generally recommend a stage two... keep in mind that the first stage is not programmed. Its merely "off".
Chip and custom prices are here:
http://www.motorhaven.com/customer/home.php?cat=37
We've done so many custom programs I've lost count, from headers to superchargers, you name it (even doing one for a turbocharged Escort soon!).
Please don't repost to get a response. The reason I'm taking longer than normal to respond is because the company is in the process of moving to a new location. That takes a lot of extra time away from me. I get to all posts, no repost is needed and it doesn't speed up responses (it causes more work).