I was troubled by the fact that not all pins on the Mega 2560 processor are wired to the input/output pins on the board. I was particularly interested in the Input Capture Pins for Timer 1 and 3. Carefully I soldered these to a fly lead and then improvised a new sockets. With a suitable input and enabling Input Capture on these timers and it all works fine.
Question - Is there any reason, other than it requires a steady hand to solder these pins, that the unwired pins on the processor cannot be used?
The hardware definition for the mega doesn't assign Arduino pins to them so you can't use the Arduino IO functions like pinMode(), digitalWrite(), digitalRead(). Of course you can always just use direct port manipulation. There is a project that provides Arduino pin definitions for all pins on the ATmega2560:
After installing, you would select Tools > Board > ATmega2560, then Tools > Pinout > AVR pinout. Note that the pin mapping is completely different between the two variants so the Arduino pin numbers for the standard pins on the Mega will also be changed.