I don't think I follow what you're saying - clocking the bits (samples) into the D/A comes well after the reading of the disc, so how does the source (CD vs. CDR) affect the quality at the point of putting it into the DAC? Are you suggesting that a CDR gets read "wrong" despite being bit-perfect where the CD gets read "right"? I also don't understand the concept of "bit phase". Would all these issues go away if the whole CDR was read into RAM before playback began?
I'm very open to the concept that CDRs are somehow inferior to the original CD, though it hasn't been my experience and runs counter to my technical understanding (which undoubtedly could be enhanced). I don't think Stereophile saying CDRs "didn't sound as good" really establishes much as there is an inherent bias there - if it really is possible to make 50 cent copies of CDs that are indistinguishable from the original (using a cheap computer no less), that's not good for Stereophile's business. I'm not saying their viewpoint can't be right, just that it doesn't mean much coming from them.
To answer the original poster's question, I'd use a computer and some easily obtainable freeware or shareware to make the copies. Cheap, easy and effective. -Kirk