Last night is was driving fairly aggressively when my 05 went into "Fail Safe Mode". The car would just limp along at this point. I shut it off and restarted and everything seems fine now.

Last weekend I did install some Flowmaster AT's and a KN & N CAI. Could this have caused this?

 

Did you use a tune with the CAI or make sure that specific CAI does not require a tune?

 

find someone with the SCT xCal II and read the DTC codes, it will tell you what went wrong, no speculation then.

 

Probably the K&n making it run lean

 

Check the Throttle body.
Mine did this once before it completly shut me down. Had to replace it under warranty.
Check the codes also is a good idea.