I'm curious as to how soon after the mods were completed, did the trouble start? I just finished installing a CAI, MRT-V2 axlebacks, and a RX Catch Can. Car runs great!
One thing I did notice while installing the CAI is the MAF is directional - in other words it could be installed backwards. There is an arrow on the MAF which I assume indicates air flow direction.
I'm just guessing though - I really don't know what could be your problem. 
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2013 1SS/RS Coupe L99, Stainless Power Works LT Headers, SCT X4 Custom Tune from RDP, CAI Inc. Air Intake w/ Apex Scoop, VMAX CNC Ported Throttle Body, Solo Axle-Back Exhaust w/ J-pipes, Apex Catch Can, Husky Splash Guards, Heritage Grille, 3D Carbon Rear Spoiler, Oracle Chrome Turn Signal Bulbs, GM Reverse Light Trim Billets, Gorilla Black Locking Lugs, Emblem Pros Retro SS Badges/Custom Retro SS Kickplates/Under-hood Bowtie, 35% window Tint, Nitto Motivo Tires (6-8-18)
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