Does anyone have any ideas why the homemade stopwatch is running too fast? Any ideas how I can fix it?
An Arduino is clocked with 16MHz. If you built your custom board with a 20MHZ clock and compile your sketches with the standard Arduino settings the complete timing is wrong.
You can add an entry in your boards.txt where you change the clock setting to 20MHz, compile again with this board chosen and your clock will even be more accurate than the UNO because you're using a crystal instead of the UNO's ceramic resonator.