If I understand well, you use 60 outputs on your Mega 2560, one for each second (led) ?!?
You can reduce it drastically using shift registers (like CD 4094) mounted in cascade. Each one has 8 outputs, so you would need 8 registers to drive 60 leds.
On the µC, it only requires 3 outputs to manage the whole:
1 data line, 1 clocking line, 1 validation line (strobe).
You have an example here, with segments displays instead of leds, but its the same (3 CD4094 in cascade):