Crystal oscillator on custom ATMega2560 board is at the wrong frequency
If the XTAL2 pin is an output (as indictaed on your schematic) then R4 needs to be in series with this pin and not XTAL1 (appears to be an input on your schematic). Without a proper value of R4 in the right place you may never get oscillations to occur. See my answers here and here explaining the various components surronding a crystal that make it oscillate.