> I occasionally saw pupae with the characteristic tongue protruding,
> these were usually at the caramel color stage

That is what I wonder about.  I occasionally see fully developed
pupae/adults dead in the capped or partially uncapped cell with the
tongue out.

Is that AFB? I half-assumed it was starvation, possibly due to some
parasite or virus affecting the ability to absorb food or preying on the
pupae.

The ones I wonder about are not at that stage, but still tan and are
dead.  They are intact and there is no ropiness.  That, I assume comes
later if it is indeed
AFB.

As for lab tests, I often wondered how well they are done and how many
spores it takes to get a positive.

NYS notwithstanding, AFB is not a black and white question, but usually
one of degree, with the breakdown being an overt stage.

There are strains of bees I have been assured that can occupy a hive
with scaly comb and clean it all up without assistance from
antibiotics.  Are such hives infected with AFB?  And when would one
declare them not?

I assume that researchers who intentionally infect larvae and watch the
disease progress should have a clearer understanding than us lowly
inspectors.

My experience is similar to yours.

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