@noduhduh said:
Only other thing I changed was instead of making my cylinder finished height (2"), I made it taller than needed and just intersected it at 2" instead. Come to think of it, that's probably what did it?
It's generally easier to do this kind of thing if you add plenty of excess length so it's easier to select and erase the unwanted geometry. And it's not like the excess geometry is costing you anything.