I know very few PhDs how got into grad school by having good grades and sending out applications.  Most professors have a certain amount of autonomy i choosing who they want as PhD students.  My girlfriend for example never applied for anything.  She did some work with a professor who then asked her if she'd ever considered doing a PhD, my girlfriend said it sounded interesting the professor filed in some papers and that was basically that.  I know a lot of other people as well who basically got in on some variation on that theme.  So if you find a professor you want to work with and that professor wants you as a PhD student then things often work themselves out.