I don't know much about TunerStudio but can you see the coil control signals? In other words does it show that the current is being turned on and turned off? That's what causes spark, the turning off of the current.
11.9 volts is low, implying that the negative side of the coil is grounded. But it should only be grounded through the Megasquirt circuit, no other circuits. You might try disconnecting the connection to Megasquirt and seeing if the coil still has a voltage drop. You might have a short to ground on the negative side of the coil. With Megasquirt disconnected from the coil the voltage should match battery voltage exactly since no currrent is flowing.
The other thing connected to the coil negative is the tachometer trigger. A shorted tachometer could cause the problem, for example, although that is unusual.
You didn't confirm that the old igntion module is completely disconnected. If the blue wire from the coil is accidentally grounded it will cause a problem like yours.