All the wiring from the ballast resistor to the coil is not used with an MSD ignition. Whether you have the ballast resitor in or out makes no difference, it's not connected to anything in the ignition circuit when the MSD is being used, same for the stock ECU.
The only wires you should have connected to the coil are the orange and black wires, orange to coil + and black to coil -. The large black wire is tied to chassis ground. You indicate that it's on a screw into the floor. Do you have a ground strap from the block to the body of the car?
If all the connections are good I would look at the pickup in the distributor.