Mustang 5.0 P0171 and P0174 DTC's

A contact very recently bought a 2013 Mustang 5.0 (6sp) that had a Bama Performance (SCT FLash) loaded. The rear O2 sensors were disabled and the car ran great. With the supplied programmer and for NY inspection he loaded the stock tune so the rear O2 sensors could cycle.

Now he is getting P0171 and P0174 (System too lean Bank 1 and 2). It has headers and an aftermarket open air intake. I assume that the O2 sensors are good because it ran fine before the stock tune was loaded.

Considering that it ran great before the stock tune was loaded would looking for intake leaks really be in order?