Not sure why you think you need the 220kohm resistor in series with the diode...if the only current load is the RTC it won't draw any more current than it requires and most RTC chips (i.e., DS1337) only require about 150 uamps when active and only about 1.5 uamps when in standby, which is the state you should leave it in before shutting down the 5v supply. At 1.5 uamps a typical 3v lithium (ie, CR2032 which has 165 mAhrs capacity) should last 110,00 hours or 12 years. Even if you leave it in active mode rather than standby it should last about 45 days.

Make sure no resistors are connected from the 3v connection to any other locations as leakage paths.