P2279 Rough idle

Recently purchased a 2012 Golf R with a stage 2+ APR tune. I got a CEL for Intake air system leak (p2279), and the engine was idling rough. It would rev to 1200RPM and then drop to 800RPM and repeat. I thought the diaphragm in the PVC/Oil separator was broken so I installed a cts turbo catch can deleting the oil separator and nothing changed. After removing the VWR Cold Air Intake (foam filter) that the car came with, I found out that there was barely any foam left on the plastic cage. Most of it had disintegrated, my guess into the only place it can go into the turbo. After removing the intake tube, there was also metal shavings found on the turbo side. There is really no room to reach in and feel around for shaft play, so assuming the worst that my turbo is on its way out and needs to be replaced, that still doesn't solve my CEL and rough idle. Spraying brake clean around all the vacuum hose connections yielded no vacuum leaks either. Boost gauge also shows -21 to -20 psi at idle as well. Unplugging the MAF doesn't change the rev surging. Any ideas on what what else I can check? Throttle body? Diverter valve?

Thanks.