Fellow retroputing enthusiast Daniel Tufvesson found a nice set of tools to convert MIDI tunes into an intermediate format, very suitable for playing with a very simple program on the hd6303 and hd6309. What I think it reveals is that my lazy approach at sound interface from the emulated YM2149 to the audio CODEC is causing some rather unpleasant artifacts.
The YM2149 core ticks along at approx 1.56 MHz. This is the rate at which the tone generators update and the final output output is made avaialable. The audio CODEC interface (shamelessly stolen from Steven Edwards FPGA Apple II project) hums along at 18.43 MHz, which is 192x the 48 kHz DAC rate. So the audio CODEC interface consumes the YM2149 output at a rate that is not related to the YM2149 output update rate. I suspect that this is where my problem is. The asynchronous nature of the sound source and the CODEC interface are causing audible uglies.
I think I'll try to find some way to derive the YM2149 clock from the audio clock chain - I think that's the most straightforward way to do it. Otherwise, some sort of interpolation filter is required, which is really beyond my ability at this point - I'm no DSP guru; I just know enough to almost be dangerous.
If anyone reading this (does anyone read these?) has any suggestions or advice, I'd welcome it!