Hi Dan,
On my monitors your song does sound a little on the muddy dark side.
Your initial message says that both the original and the MP3 sounded good through your computer system regardless if listening by headphones or monitors. This to me sounds like you have some kind of EQ set up in the listening mode of your music computer. What software are you using when listening? I had the identical problem once when I was using Windows Media Player. I had set the 10 band EQ up for a song and forgot to reset it at flat response. All of my songs were then set up to sound good on an EQed playback but they sounded very bad on other machines.
As far as additional software for mixing ToonTracks EZMix
http://www.toontrack.com/products.asp?item=69 may be a good place to start. I use this quite a bit.
I forget but are you using Sonar? If so I may have some additional tips on mixing I can share with you. Feel free to ask.
After thought – I’m assuming that your headphones and monitors give a flat response, i.e. both are good quality units. If not you could be getting a false reading on both.