Hello Lowrider.
I think that the very best thing is to get the OP quickly and cheaply to a good place, where he is motivated to find the root cause. I certainly agree that the root cause is the big prize, but it may also be a big challenge.
Should have mentioned above: the best place to insert the signal isolation transformers is on the amplifier input. That removes any nasties upchain, no matter what their origin. If sound improves, and it almost certainly will, then the transformers can be moved to the CD output. If the sound remains the same, the problem is the digital source, and the OP should seriously consider an alternative, like analogue.
For example, my current analogue brightness problem is a big challenge. I am finding that two resonances were destructively interfering in my analogue front end, and when I removed one of them, detail improved, but the sound became unacceptably bright. Am currently dealing with selectively damping each one, so that I get back to an acceptable level of brightness while retaining the increased detail. I followed my own advice (above), and changed capacitors and loading resistors to reduce brightness, which was quick and cheap, because my electronics are home brew. For what it's worth, I now realize that the two interfering resonances were affecting tracking, or introducing distortion which sounded like mistracking - don't know which yet.