Because I'm 1-2 coats into the project, I think my plan now is to apply
a very thin coat of polyshades using a foam brush and just let it dry.

I assume the polyshades is oil-based. Make sure you add a little thinner.
The lower viscosity is what makes putting on a thin coat easy. Start with
about 10% thinner and add a little more if it seems necessary.

Hopefully one more coat will do it. Afterwards, I'm going to apply a
coat or two of clearcoat, "sanding" with steel wool between coats.

Clear coat, in this case is the same thing as the top coat except withou a
little color. You don't need it.

Hopefully this will clear out the color inconsistencies and not require
me to strip everything i've done so far. Seem reasonable?

Yup.