Thanks Reynard and fatmike. I've been running the Griots at top speed, but went back and kept at it with more polish and a little less pressure for more pad-speed. I've also sprayed water on while I've been polishing. It's taken a couple of hours, but that's gotten most of the spots out of the front trunk and fender tops. The paint's not perfect, but it's a heckuva lot better than it was, and I still have several other things to do on it (applying Werkstatt Prime Strong, then Acrylic Jett Trigger to seal the paint. Then tomorrow I'll start waxing. Then it'll be time to pull out the lawn chair.
It's kind of weird. I'm pretty sure these are water spots since they're only on the horizontal surfaces and not on the sides of the car. But on the back trunk, there are only the normal swirl marks that I shouldn't have any trouble with. It's like half the car was under cover or it was only half-waxed.