How important is it to completely even out the part when sanding? I have a stubborn part that has a hard time leveling out, and after multiple sands and epoxy layers, it's not sticking well and letting me sand it level. Will adding clear coat cover this? or will it show through?

Don't bother sanding it down smooth if your going to clear coat.

Fill the low spots with APF7 its a black filler for carbon then 800 and clearcoat you will never see the spots of filler

Don't bother with the smoother grades of paper its a waste of time if your clearcoating,not if your polishing the carbon thou