By coax, I presume that you are referring to the stereo analog cables. As far as "purity" of signal in this case, there is essentially no difference between digital audio between CD player and 950 (assuming that we're leaving the 950 in stereo mode) and analog audio from CD player with the 950 in stereo bypass mode -- in both cases, the digital to analog conversion only takes place once. The only question is which component is best at handling that D-to-A conversion. With most CD players, I tend to suggest using the digital audio output and use the CD player purely as a transport -- in my experience (including Yamaha and Harman Kardon CD changers), the 950's DACs are better than most mass market CD player DACs. With a Meridian player, however, the analog stage may be a step above the 950's, in which case using the analog cables and the 950's Stereo Bypass mode may provide the best results. The most sure-fire method to determine which is best in your case is to connect the Meridian to the 950 using analog audio
and digital audio, spend some time listening to both digital input and stereo bypass analog input, and decide which you prefer. Basically, there is no "wrong" answer, just the answer that you like most. As an aside (something that you may already be aware of), if you set up the "CD" input to use the applicable digital input but also connect the analog cables to the CD input, selecting "stereo bypass" works exactly as it would if you had the "CD" input set to use the analog input only. It isn't anything too earth-shattering, but makes this sort of comparison pretty simple.
Since the Pioneer 45A is a universal player, I'm guessing that you're using the six-channel input for DVD-Audio & SACD and the digital input for DVD-Video...
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