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I'd disagree about the fuel pump not being an issue, most of the 8th gens with high mileage that I've come across have had a failing OE Denso fuel pump, and replacement with a new Denso pump was an easy fix.
I haven't seen a fuel pump be the sole reason for running lean or a P0171 code, but it is possible for a weak pump and dirty/clogged injector to combine and be a limiting factor to getting enough fuel to one cylinder, at least enough to throw a code, even if it's no happening consistently or just under heavy acceleration.
Dependiing on mileage, a new fuel pump can be worth it anyway, just for the restoration in performance/acceleration, plus you can keep the old one as a spare.
Usually the P0171 is an air/vaccum leak, so you really need to check and double check and triple check ALL the hoses going to the throttle body, air cleaner, etc. Sometimes there's a cut in the rubber or even just cracks in the end of a hose that allow air in. Just like with the intake manifold gasket, sometimes the paper thin factory gasket for the throttle body needs to be replaced with a newer one to give an airtight seal.
You might also make sure you're running OE parts as necessary. As in, only Denso or NGK Iridium spark plugs. OE Toyota PCV valve. Maybe even Toyota or Denso air filter in case a cheapo brand one is overly restrictive. Sometimes aftermarket parts for fuel/ignition/etc. give weird problems and codes that go away when the OE stuff is used instead.