sbright33:
I'm not suggesting we change any hardware. I'm talking about calibrating it in the code.
I think I know what you are getting at. In the olden days ships used to carry chronometers for navigation. Now the important thing was not that they showed the correct time of day. The important thing was that any error they had was a constant error. For example, if the clock lost a minute (exactly) a day, then you could compensate by adding one minute per day you were at sea. So this in effect is a "code calibration".
Also, interrupts should not affect the internal timer. It is running in the background anyway (it's a bit of hardware). Doing serial reads or serial prints should not affect it at all.