What's the weak link in my system?

@jdm11 - I totally understand. I had to leave for several hours, but before I left I just saw how you described what your "problems" were and what you wanted:

- CDs sound a bit harsh and thin.

- I’m looking for a more "3D" kind of sound with depth and warmth but clarity as well (not muddled or fuzzy).

If these are your problems, there are several things I can think of that could help you move towards your goal:

- power cords. If you are still using the stock power cords for your equipment (cd, preamp, amplifier), then looking at an upgraded power cord can significantly improve things. I have recently found that the Audioquest power cords which use solid-core conductors are an excellent solution. I listened to the Audioquest NRG-4 model before I re-terminated the ends with Furutech rhodium connectors. The stock NRG-4 cable sounds very nice. It has a very solid sound with warmth and power. The solid-core conductors ensure that music impacts hit with authority and power. The gold-plated copper connectors give a nice warm sound. I would avoid any of the power cords with silver-plated connectors in your situation.  I have gone through testing with many different power cord material and geometries.  Solid-core conductors win every time.  Stranded wire power cords can sound good, but they just don't have the same "solid" audio character and they sound very "lo-fi" and "digital".  I have tested this with a very high end Furutech OCC copper power cord.  They just don't work as well as solid-core conductors.

Stock power cords usually use very small 18awg stranded conductors and may not even be copper. The stock cord connectors are also poor quality. These stock power cords can introduce a bright/harsh character to the sound.

- fuse upgrade. This is only a slight suggestion as fuses are definitely a controversial subject. I have also found that stock fuses will sound bright/harsh. Although, the right choice of fuse can be difficult to determine. I usually recommend Isoclean as being a very nice warm sounding fuse. This may end up being to warm for you as it can roll-off the high frequencies in some scenarios. You can try the Furutech/PADIS fuses, but expect a 200+ hour burn-in and these fuses can be very fast and revealing to the point where the system becomes too thin/lean/cold. There are other fuse choices. I would avoid the silver Hi-Fi Tuning fuses in your situation because you feel you have too much harshness/thin character.

- Interconnects. If you want, you can start backing off from the silver-plated elements. Your Audioquest Diamondback interconnects have excellent conductors, but they do have the silver-plated connectors. These will conduct electricity a lot faster than other elements and will contribute to the very bright/thin character. If you want to look into this, I would say to get the best Audioquest interconnects you can that still use gold-plated connectors. The Perfect Surface Copper and Foamed Polyethylene Insulation are excellent items in Audioquest cables.

- switching power supplies. All of your listed equipment uses linear power supplies, but you don’t describe power distribution. Are you using a single power strip or going to different outlets? If you have any device with a switching power supply connected to the same power strip or outlet, this can cause your audio to have a bright/harsh digital solid-state character. These can be things such as bluray players, satellite receivers, or anything else that has a switching power supply or wall-wart.