Since your using the shiny egg time finder, you dont have to worry about capturing pokemon.
To do a delay and second calibration, you will have to set your ds to a external clock.
Then you will start your game
Then once the time becomes the next min (example it was 1:51:59 and became 1:52:00) you will soft-resetting a rapidly press A until you enter the world
then you will capture a high level pokemon and input the information in the seed finder
then you will click find and 1 set of delay and second should appear.
You would then record the delay and seconds and repeat the process again about 9 more times. From the list you will have calibrated your seconds and time.