P0171 code driving me crazy, HELP! :)

So, my 2005 CE is throwing a P0171 code (bank 1 lean).

I've replaced the Mass Air Flow sensor, I've had the intake smoke tested and sealed, I've replaced the downstream O2 sensor, I've replaced the upstream Air/Fuel Ration sensor, I've replaced the PCV Valve. It's still throwing the code.

I'm running out of ideas.
Been having the same code plus 0441. Mine is 2006 5 speed standard. Started acting strange hesitating and bucking at neutral throttle going 40 or so and after I would fill it up. to start it I would have to put my foot on the throttle or it would stall. After getting into 3rd gear it would act normal and not stall anymore when I released the pedal. now thats not to say 3 gear had anything to do with it normalizing just took that long to get back to normal or s it would seem.
I replaced the mass air flow sensor and the not starting after a fill up went away but the bucking and hesitation at neutral throttle has persisted. I hope I'm making sense to someone cause its getting frustrating for sure. I I like my Carolla got it new with 5 miles on it and now has over 260k. been no trouble till now. Any help would be greatly appreciated.