Correct AFR for E0 (100% gasoline) is around 14.7, E10 is around 14.2. your 14.7 is just a bit lean 3.5% for E10 or .5% rich for E0 , I assume your running E10. So your AFR is good.
Remember the PCM does about anything possible to correct an incorrect fuel burn. Beyond keeping the engine running, emissions are its main mission. The P0171 says your PCM is adding over 14% extra fuel to make up for a sensed lean condition. Since it's adding the fuel to correct the burn the O2 readings and any AFR measurements would show results of the correction. If your AFR is truly 14.7 then the PCM is doing it's job correctly to fix something wrong. I asked where you got the reading as that's important was it a wideband AFR or something else, from what I've seen the PCM does not report AFR. It reports LT and ST Trims. Those readings are critical to seeing what's happening. LT trims tell the percentage of fuel the PCM is adding/subtracting and ST trims show the results of the fuel addition (actual burn). ST s/b +/- 5% or lower , LT should not exceed +/- 10%. (0-5% is good) LT exceeding +14% throws the P0171.. for trivia a LT trim of -35% (pulling fuel) rich throws a P0172 the PCM tolerates pulling fuel much more liberally than adding.
Was the truck running error free before the tune, and was it untouched (no mods) between tunes ? . If so have you contacted your tuner.. as asked in post #4 does the tuner know about you custom air intake box. You could have been running 13% lean before the tune and the alterations took it over the mark, Any chance you know what LT trims were before the tune...