To follow up on this, if I'm careful and I create activities one at a time and don't dupe them and don't drag them around, everything is fine. I'll be duping courses later today so we'll see how that goes, but I suspect since each original course is clean it won't be an issue.
But, I think the system needs to be tweaked and that the grades should ALWAYS follow the order of the course itself unless an admin overrides the order on the back end. And then, if you're going to continue to use the IDs that you currently use in the db, moodle needs to be able to reassign the entire table to actually let you re-order things...OR, that ID needs to be dumped and some sort of smart ID that is tied to the course needs to be used instead so that the order of the table doesn't matter.
Hope that makes sense. I'm not a programmer, I just know it was pretty easy to break the grading order and there was no way to fix it in the admin short of starting over.
