Scott,
I don't know how good the DAC in the SP2 is compared to what you used previously, but my guess is that the Airport Express could be the weak link in your fairly capable system. I have three Airport Express around the house, but use them for less critical listening than the main system.
The main system uses coaxial S/PDIF from computer soundcard into the DAC. I did compare the optical from the Airport Express and did not think it sounded as good. The Airport Express is generally considered to be a higher jitter optical source than that from the Mac Mini, and that's what I speculated might be responsible for the loss in focus and clarity. I didn't have any additional distortion, but the loss in detail was analagous to a camera lens just slightly out of focus and may be what you're also referring to as "muddiness". I think it becomes easier to hear a loss of resolution as the volume increases.
For a little time spent but no monetary investment, it might be a worthwile test to try the mini directly connected to the SP2 to see if you can hear a difference.
If it turns out the Airport Express is the limiting factor in your setup, I'm not sure what the best wireless alternatives would be. The Squeezebox Touch is no longer available new from Logitech, and the Bryston BDP-1 player (with separate outboard Ethernet > WiFi adapter) would be a serious monetary investment. A second Mac Mini run headless connected directly to the SP2 may also be a viable less expensive option.
Steve