This might be an overly-obvious suggestion, but have you checked (with an audio editor program) that you're using most of the available recording range? That is, are peaks on the signal up near the maximum level possible given your recording depth? If not, you need to adjust the input sensitivity of the ADC to match the output level of your tuner. This gain matching is critical to getting a decent recording - you're just throwing away bits if your peaks aren't NEAR digimax.
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