Thought I should write a bit of an update.
Assembled the first board and had issues from the word go - power correct everywhere, but 2560 no worky. Long story short, the atMega2560 processor on that board was dead for some reason. External clock, new crystal etc, nothing seemed to get it talking. Putting it down to a 1 in a million failure - who knows. Removed the 2560 from the board and will order another chip in to replace it.
Assembled the second board, and smooth sailing so far - phew, for the most part anyway.
Tested the following things, without issues - very crude code, just to prove the hardware
2560 bootloaded and fused correctly, and USB programming working.
Relay Outputs - all 6 switch fine.
General IO - all 18 as inputs trigger as inputs no problem. Even applied 18VDC to one of the inputs, and it lived - yay.
Analog Outputs - all 4 appear to work no problem with the library found on here.
Analog Inputs - all 8 appear to work no problem too, thanks for the help RetroLefty.
Digital/PWM Outputs - all 12 appear to turn on and off, havent put much effort into making the 16 bit capable PWMs run at 16 bit yet, but thats software really.
Bluetooth - connected my Sena module and with my very crude code echoed the response to the USB so I could see whats going on, so that works. Data flowing to laptop terminal program.
SPI to atTiny84's - Got comms working with the help of Graynomad and Nick Gammon - thanks, so have the USI working in SPI mode, and can pass data between the 2560 and the atTiny's. High Speed code, as per the intension of the atTiny's, I dont have working yet. Currently trying to get that working.
Still to test:
XBEE (Dont own a XBee yet...)
So great result so far, just time consuming testing everything as Im not much of a coder, but eventually get there. On about the 4th 2am finishes with 6am start for work - so getting a bit tired, but must...push.... on....