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.
