Indeed the gasket had nothing to do with it, a little carbon will leak out with moisture leaking out and that does not equate to sound leaking when the system is hot. Since you have sealed it all up and it made no difference, you already know this now.
Break in period at least a 1000 miles, it's a process of all the highly reflective metal surfaces getting coated with carbon. If you take a lot of short trips it can be less than 1000 miles, but if your daily drive is long, then the motor is running efficiently most of the time and not making a lot of carbon and break-in time can end up being a few thousand miles. A number of other variables impact the process including fuel quality, state of tune on your Miata, etc.
Other than wait for further carbon coating of inside of the system, which will change the natural resonance in the system, the only other choice is adding a quarter wave pipe or helmholtz resonator (see Synapse NoDrone