So after 4-5 hours of hand polishing with ZPC, then Z-2, Z-5 and Z-6 the swirls all went away. I polished my car and viewed in direct sunlight several times to confirm.

I wonder if the swirls have always been there and I've never noticed before. Usually when I polish, I don't bother checking in direct sunlight.

I also wonder, if some of the swirls are just being filled. I only used ZPC (which is midly abrasive) on the rear hatch. On the hard top which also had swirls I just used Z-2, Z-5 and Z-6. gfspencer is right as well about flat vs. curved surfaces. With a shop light you can see the swirls.

I guess I'll find out in a few weeks when the polish begins to wear off.