i went through this same problem with my motor, it turned out to be the positive wire from the MSD box to factory ignition wire it was hooked into ky hot, not a const hot once the car is running, so its getting signals, but not a steady signal....also make sure you have a good ground....make sure your coil is not on an angel, (some are filled with gel on the bottom to make a solid connection.
its hard for me to word it, but its something to do with your ignition wire from the firewall
