Reading through all of this, the only thing I can see for certain is that you really don't know what the problem is. Sure, it can be the cables, amp, preamp, room acoustics, tubes, power, sources or speakers, but unless you have other components laying around that you can swap out, you may want to start eliminating some of the potential causes to your problem.
Looking at your system, I would say that using your PC as a source is the most likely place for something to go wrong. I would start there. Take the CD's that you ripped and find a CD or DVD player that has a digital out. Most do and it doesn't have to be anything expensive. Try using that as a transport going to your DAC instead of the computer. Don't change anything else. After trying that, was it a step in the right direction?
Looking at your system, I would say that using your PC as a source is the most likely place for something to go wrong. I would start there. Take the CD's that you ripped and find a CD or DVD player that has a digital out. Most do and it doesn't have to be anything expensive. Try using that as a transport going to your DAC instead of the computer. Don't change anything else. After trying that, was it a step in the right direction?