Hey guys just a hunch but did your pro tuner remember to disable the P006A DTC in your tune? lager MAF housings and boost will cause instant limp mode if this code isn't disabled. I'm running custom 3" intakes and had a hell of a time getting around a similar issue. The worst part is it'll go into limp mode without a hard code, just a soft code in the background so no CEL will come on. The new version of Uprev removed the DTC toggles so your new ROM might be missing the toggles to dissable the P006A but ProTuners should be able to work around this. If you want you can even send me your ROM and I can take a look.
Also I remember reading somewhere about an issue with the intake pipe near the filters on SC kits. Something about an adapter of some sort not fitting right and causing improper air flow around the MAFs. Double check your fitment and make sure everything is good.
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