Headers and crossover pipe with RoushCharger

If you did short tube headers and a catted mid pipe, there is a chance you would be ok, but even that might not work. Short tube headers are not known for giving any significant power gain in 05+ mustangs. If you went with long tubes and an off road mid pipe, then you would definitely need a tune. I don't think you can send it back to Roush for a tune like that, you would need to get a custom tune. You lose your Roush warranty as soon as you do stuff like that. Brenspeed and Bamachips seem to have the best reputation for mailed tunes, but the safest way to go is to get a custom dyno tune.

I have experience in this field. It's not difficult at all to remedy your situation with the right equipment.

As stated earlier, stick with the catted-pipe and you shouldn't have any major issues.

I can tell by the way that you phrased your original question that your intention is to remove the catalytic converters. The short tube headers won't effect anything on their own. It's the cat-less midpipe that throws off your sensor data.

You will need to upload your stock rousch tune to a tuner. I use HPTuners and you can use it to modify Rousch tunes, not sure if the SCT can or not. What you will then need to do is disable the rear O2 sensors, and then disable the catalytic converter overtemperature protection, called COT. You will also need to make an approximately 2% richer air fuel mixture at idle, not WOT. It's all easy minor changes when you have the right equipment. I have done this on a car that had the rouch charger added to it (it was originally a stage 1) and then had rousch flash their tune on it. I have to say, their tune is pretty darn good, but I was able to coax another 18-25rwhp out of the ENTIRE powerband on it without making any drastic changes, and that was in addition to the modifications.

Some of the other changes to make while in there tuning:

Their tune commands a 11.72:1 AFR, you can set this around 11.95:1 up to 12.05:1
Set spark to match the MBT tables for maximum timing, with the exception of the bottom left corner of the table. (assuming you don't knock)
Remove Octane Plug modifier
Change Throttle Position Max to 82% on the entire RPM range.

There are some other tweaks, but those are good ones.

The shorttube headers really don't do MUCH, even on the supercharged cars. If this were another car it would be a different story, but we are all fortunate enough to haev good manifolds. If you want short tubes let me know. I have an unused set I can sell you cheaper than the sale prices on the other sites. I bought them and then realized my car was already WAY to loud after the other exhaust mods I did.

You will gain some power from the Catless X-pipe, but you're looking in the ~10rwhp range, and you have to make the changes for COT like I mentioned.......oh, and I forgot you have to turn off codes P0420 and P0421 for the catalytic efficiency codes.

With a Cat-less x-pipe and the right axle back be prepared for some ROARing exhaust. If I had a video camera of my straight pipe setup I'm sure there would be some guys out there FAPPING under their desk.

Here's a poor vid of an In-cabin Startup of my car: http://video.google.com/videoplay?docid=-4984408711277321666

When I put my long tube JBA headers and high flow cats on, I did not have to re-flash. The original Roush tune worked just fine.