Misfire at cruise, popping/afterfire at 3000RPM

Is this a new build, or did it just recently start misbehaving?

If it were me, I'd pull the valve covers and rockers shafts/pushrods. It wouldn't take long and would tell you real quick if something is fubar up top. I've seen issues like this before turn out to be a bad cam, bad rocker arms, failed lifters, etc. The issue being present when revving in neutral is what makes me suspect valvetrain.

These types of issues are often easy to spot with the valve covers off, and especially if you crank the motor over (with ignition disconnected!) and watch the rockers.
You could also set TDC on #1 and watch the springs as you remove the rocker shaft and see if any of the valves are being held open somehow. At any rate, lots to see and determine under those valve covers.

Not that anyone above is off the mark, but no amount of ignition fiddling will fix a mechanical problem, then again no amount of mechanical fiddling will fix an ignition problem either!