SD Card Shield configuration on Arduino mega 2560 REV3?

What is stopWatch pin? Its pin number?

Which SD library are you using, the adafruit SD library or the arduino IDE SD library? Do you have an SD library from adafruit on your computer? There is a version of adafruit SD library that can use software SPI on pins 11-13 to save their areses for their SD logger shield but you should NOT use software SPI.