I doubt it is afr or tune related and agree with BWill, especially with your description of the cars symptoms. Many of the members are running CAI's (SRI's like yours but with a heat shield) and aren't experiencing those issues. Even the most highly modded member is still running within AFR parameters, albeit a bit closer to lean than most.
The two things that I would try is using 93 octane and disconnecting your battery to reset the LTFT'S. If neither of these help, try to find some members running the FSWerks or Steeda without the shield and send them a PM to see if they are experiencing the same issue.
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