If your Roush was bone stock there should be no reason to do anything to the tune. (On the surface). Roush's tune will be the absolute best option for all around driving and power. With the factory tune it should run well whether in sub-zero conditions or in desert heat, racing or cruising, all day, every day.
The lean A/F condition / code, with the car in 100% stock form, was due to something else, possibly a vacuum leak letting in unmetered air, a failed O2 Sensor, maybe a bad MAF. But there are diagnostic trouble codes for failed O2 and Failed MAF. So if you get a check engine light it is important to get the codes by going to a local auto parts store and having them read the car through a scanner connected to your OBD port. (unless you have a programmer already... More on that below).
Once you start modding the car... Changing exhaust pipes, deleting cats, larger intake tubes, s/c or crank pulleys, etc... You will might need an adjustment to the tune. Some changes are minor enough that the computer can compensate, but it can only adjust so far before it thinks that something is wrong and turns on the check engine light.
Now combine a possible pre-existing issue with the addition of modifications and it makes it very hard for any of us to help you without very specific details.
The A/F shouldn't be way off with the little things you've done. There has to be more to this. Did you or anyone else change the pulley on the supercharger or crank? Did you change the air intake tube? Those specific mods are very likely to cause a lean condition due to the increased air flow into the engine.
Did the car come with a handheld tuner? If so... Then someone has already changed the tune. And you can read the DTC's yourself and post the codes you are getting.
We can get to the bottom of this.
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