Did you install a tune to match your CAI. You mentioned using the tuner to pull code, but no mention of installing a new tune. Just curious, as this could be the problem. Also make sure the MAF is installed the right way around. Some have managed to put it in backwards causing all kinds of problems. The little window with the sensor wire inside should face the incoming air flow. Also check for vacuum leaks at any point that you had dissembled. Good luck.
2005 black GT premium (5spd) / GT500 front LCA/upper strut mounts / Koni Adjustable (yellow)shocks with Roush Springs / FRPP 4:10 rear gear / BMR rear UCA/LCA+relocation brackets / MGW Shifter / Bassani axle backs / Cervinis heat extractor hood and Ducktail spoiler / Carroll Shelby CS69 20x9/20x10 wheels / MSD Blaster 2 coils / Roush TVS2300 Supercharger+Brenspeed 560R upgrade / Exedy Mach 500 Stage 3 Clutch / Exedy lightweight flywheel / SR Performance braided stainless clutch Line / Afco Dual Fan Heat Exchanger upgrade / JLT Catch Can / Axle Exchange one piece aluminum DS / Silly grin on my face every time I turn the key.