The Fcon tune doesn't change, in fuel or timing and the stock ecu has no control over either, only the cams and throttle. The Fcon will adjust your cruise/light load AFR's using the stock o2 sensor if it is enabled in the tune, but mine doesn't do that so I can't really help. Best to speak to your tuner.
Mine has been in fault for years, are you really that worried the engine light is up? Remember you have essentially cut the stock ecu out of the equation, it is bound to get cranky.
The pinking won't be fuel related, it will be timing. Again, speak to your tuner and tell him what it is doing and when, all it will need is a little timing backed out in those low revs.