Its difficult to define a noise with written words... you might peruse my post on diesel pre-ignition to see if there are any tidbits of wisdom there. Is the noise like what you get when you throw 87 octane ( or bad gas) in the blown Miata?

Sure fire way to see is to add some cetane boost to the fuel, or add bio. I have a heavy mix (16 ozs to 20 gals) of cetane boost in the car now, as well as reconnecting the EGR and the issue is mitigated, but not gone. Biofuel ( with a cetane north of 50) is the next step.

If its an pre-ignition engine noise, try cetane boost and see if it helps.

I'm also going to see if I can richen the mixture at part throttle by adjusting that "hat" thingy. When I figure out exactly what that " hat thingy" on top of the IP actually does.

It could be something as simple as an exhuast leak, which even at idle, with a 3' small rubber tube ( winshield washer size) in your ear as a stethoscope, you'll be able to discern.