Question

Will Inner Focus work with Focus Punch?

Answer 1

I'm not sure you understand how Focus Punch works.

Inner Focus merely prevents the Pokémon with the ability from flinching.

Focus Punch will fail if the user is hit by an attack before it can hit the target.

Focus Punch failing (the user losing it's focus) is not the same thing as flinching, so no Inner Focus will not make Focus Punch hit 100% of the time.

Answer 2

No, it won't.

Inner focus just makes you unable to flinch, you still get hit.

>Inner Focus prevents the Pokémon from flinching. Pokémon with this Ability can still flinch due to a Pokémon with Mold Breaker, Teravolt or Turboblaze.

Focus punch will always fail if you get hit, not if you flinch. Any move will fail if you flinch.

>The user of Focus Punch will charge up during the beginning of the turn it is executed, then attack at the end unless it is hit by another Pokémon's attack before launching its own; in which case it will lose its focus and be unable to attack that round.

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Source: Links above
Hope I helped.