datalogger for counter sensor with RTC HELP!

I really haven't read the entire post, really sleepy right now... but did saw one thing that disturbed me...

//SD Card will Draw Power from Pin 8, so set it high

pinMode(pow_pin, OUTPUT); 
  digitalWrite(pow_pin, HIGH);

DO NOT use digital pins as power supplies. Use controllable voltage regulator or a MOSFET switch circuit. You could find a lot in google about those two terms. The idea is to use the digital pin as a "flag" to tell whether the "switch" should be open or closed. Using digital pins as power supplies could and probably would destroy your peripheral device (that is being powered) and definitely your arduino board.

Your SD card, depending on the speed class could draw more then the limit of 40mAh of the digital pins.