Thanks, Dov.
I went in to Font Book again, deleted the first Futura Bold (licensed) and restarted. Now InDesign looks for that font when I open the file, and I'm able to remap the missing font to my new, purchased Futura Medium BT.
But that doesn't explain why my color fills are solid black. And they're not placed graphics, they're rectangular shapes in InDesign.
I'm using the default PDF settings for print.
Anyone?