I'm not able to smelt iron/copper ore (pure form after being sorted) in a stone furnace. FNEI is saying the ores can be smelted, but hovering over the input slot on a stone furnace says they can only smelt the crushed B/A ores. Am I missing something? Is there another way to smelt the pure ores?

The recipe is disabled. The way to smelt iron plates is to either use the recipe for crushed saphirite or to use the B/A smelting facilities to go the ingot -> molten iron route.
I would suggest to disable "Show disabled recipes" in the FNEI settings to prevent such a confusion. The recipe you see is the vanilla iron plate recipe you are not supposed to be able to use.

I think you dont have checked in mod settings Starting resources Saphirite, Stiratite, Bobmonium and Rubyte. You cant smelt anything without this ores in starting area and must expand in start.

You can also smelt via PY refined iron/copper, which is very early and easy to research