The ignition really depends on how you setup the crankshaft. Do you have two cylinders in the same phase, three different phases, or some sort of odd-fire setup?
If you are sticking with an OEM style crankshaft with an extra pin,rod, and cheek scabbed on, then you can use an OEM ignition setup, and just need yo use an aftermarket triple wire output coil (common for outbard marine engines).
If you want to get more exotic, then the sky is the limit.