If you don't have a tuner, you can take your car to the local Autozone or Advance Auto and use their code scanner for free. Whatever code comes up should lead you in the right direction of what malfunctioned to cause the CEL to activate. Then, you can use the scanner to clear your fault code(s).
disconnecting the negative battery terminal and reconnecting it also clears codes. mine would pop up from time to time before i turned of the rear o2 sensers
I've got a hand held scanner but it read error, so I contacted Roush about it because I saw on the PCM a sticker that they had recalibrated for the roushcharger, they said take it to a dealer who sells Roush products.
I had a customer have the same problem trying an SCT scanner on his rouschcharger. We were able to retune it with HPTuners and get 25rwhp out of the entire curve.