After several days of playing with the Mac Mini and Pure Music trail I have decided to keep it and get the full version of Pure Music when the trail expires. This is my first time using a dedicated computer for music (my main computer is a mid-tower custom built desktop running Windows 7 and JRiver), and I am happy to report that the Mac Mini and Pure Music combo is a great experience. I am controlling playback with the Remote app on my iPad, and using OS X's Screen Sharing and VNC Viewer on the iPad as a screen/keyboard/mouse.
Regarding the USB ports, after more listening I think Port #4 (closest to the SD card reader) seems brighter and has more sparkle in the treble region, which probably gives the perception of better clarity that I mentioned in my original post. But Port #1 (closest to the power switch) sounds smoother, has a darker background, deeper soundstage, and more music seems more enjoyable and flows more easily. I think I will stay with Port #1. Theoretically, Port #1 should sound the best because according to System Information (in the Applications --> Utilities folder), Ports #1 and #2 shares resources with the IR Receiver (which I turned off), and Ports #3 and #4 shares resources with the Bluetooth receiver (I left that on for the keyboard/mouse in case I need it, and to wake the computer). The port that the USB DAC is connected to should not share resources with other devices, right?
Anyone else tried the different USB ports on the Mac Mini? Would be nice to hear your thoughts.
EDIT: My father decided to keep using his dedicated Lenovo Thinkpad as his media server (music and movies) running JRiver; that is why the above comments were "I" instead of "we" or "him."
EDIT 2: My current system is: Mac Mini with Pure Music (native sample rate; no upsampling); music is stored on a Firewire 800 external hard drive that has its own power supply --> Wireworld Silver Starlight USB cable --> T+A DAC 8 (Beyerdynamics T1 connected to the DAC 8's headphone out) --> Straightwire Serenade II interconnects --> Octave V70SE tube integrated amplifier --> Straightwire Serenade II speaker cables --> Dynaudio Contour S3.4 speakers.