I etched my floor with muratic acid per the instructions but it is not consistent, there are still sections that seem smooth. Do I redo until roughed up everywhere?
Doesn’t need to be ‘rough’. You just need water to be able to penetrate and not sit at the surface. ‘Roughness’ isn’t a factor for a coatings suitability to adhere.
Etching really doesn't physically change the floor much since the etching is at microscopic levels, it's probably fine.
But..if the floor has an uneven finish prime, as a single epoxy layer alone will most likely soak in unevenly and not give a uniform finish unless primed.