Secondary air pump hose goes to the secondary air pump. You should have a breather filter on that if you are using a cone intake. I dont think a cone intake will hurt your engine, but it sounds like you might just have a dirty/bad maf if you didnt use oil on the filter. Try cleaning it with electronics cleaner or alchohol. Youll see the metal sensor in the protruding plastic part. Try to geta soft brush in there and clean it. Just spraying/soaking the sensor with cleaner doesnt normally work, at least for long term. I wouldnt bother washing the filter. I doubt just going back to stock airbox is going to solve your CEL/lean issue. What exaclty were the fault codes?