Rotor phasing is correct, that was one of the first things we checked. With balancer at TDC, the rotor is just behind the #1 terminal in the distributor, both the intake and exhaust valves are closed.
We're not talking about the engine--to rotor mechanical relationship, we're talking about the polarity of the crank trigger pulse, as well as mechanical positioning of the crank trigger in relation to the rotor.
The only way to check it especially with a crank trigger is with a cut--open cap and a timing light.
In other words the crank trigger causes the ignition to fire at some point in time, and if the MSD system has electronic retard, then THAT comes into play. But wherever the spark happens in time, the rotor must be lined up with the distributor contacts in that instant in time