I'm assuming that you remove the interior door panel to remove those tweeters.

As for cutting the cups, if it was me I'd use my drill (seriously) as I don't have access to a rotozip, dremel, etc. It works, I once used that method to modify an airbox. Just used cable cutters to clean up the edges.
Just be sure that with the new speakers sticking farther into the door, that there won't be any clearance issues with the window when it's down.