*UPDATE*
I had what i thought was a separate issue with the battery light occasionally coming on while operating at lower rpm. The truck died on me one night so I tested my batteries and checked the pigtail to the alternator both checked out ok. So I went ahead and replaced my alternator and...
Thanks everyone, sorry I didn't include earlier my codes consist of:
P0046-t/super charger boost ctrl solenois circ range/perf
P0404-exhaust gas recirculation circ range/perf
P0460-fuel tank level indicator circ error
P0528-fan speed sens circ no signal
P1000-monitor checks not complete
I...
I have a 2006 f250 cclb with the 6.0L, mods: fuel economy tune (super chips device(yes I am getting an sct i just had the super chips from my previous truck)) exhaust was ripped of just after downpipe, under heavy acceleration and on cold mornings I get a good sized cloud of white/grey smoke...