The only way to run Megasquirt properly is to convert the ignition to Ford's EDIS-4 system.
You can find EDIS-4 kits on ebay and other various sites.
It involves fitting a toothed 36-1 wheel to your crank pully then mounting a vr sensor that will pick up the signal and send it to the EDIS ignition module, the module then sends a signal to megasquirt that is returned to the module which then fires the EDIS coilpacks.
Most kits come with a toothed wheel, the vr sensor, ignition module, coilpack and wires (you need to convert your spark plug wires to connect to the ford coilpack because its a special connector)
I haven't researched anything else since i was already familiar with megasquirt, but im sure there are other kinds of ecu's out there.