Hi Mate
There are no timing marks as this is a modern engine and the ignition timing is determined by the holes in the flywheel and the injection timing is determined by the cam sensor/crank sensor. It's exactly the same with your proposed megasquirt, the timing and injection will be determined by the crank sensor and whatever you programme into the megasquirt. If you are timing the engine for a cambelt change there is a pin tool that locates the crankshaft at TDC on 1 or 4 and a plate tool that locates the camshafts at TDC on 1 but this is only with the engine static.
Barry