If you are running Server 2003, I'm going to assume you are somewhat computer literate. Have you tried a VM with an XP or 7 install?
The list of software incompatibilities with Server 2003 is pretty long. I'm surprised you've made it this far. Good job.
I already had WMP11 installed. And configured to use Windows Media Sharing to stream to the Xbox. The latter was the hard part, having to install SSDP and UPNP wasn't easy (until the second time I did it when I found someone's rundown on how to do it). Installing Zune itself was pretty effortless as well.
I could probably figure out this issue with a dependency list myself, but now I don't have time to toy with stuff like that anymore.
I have got the sync working on a Windows 7 laptop, so it's not an issue with the phone.
Two other complications -- I moved in with my girlfriend and my computer is still at my mom's. I have been waiting until I can get someone with a truck to move the desk. That runs 2008 server (which I kind of need for my personal development projects), and while there may be some install check edits needed to install Zune, everything else should just work as expected.
The other problem is the CD ROM drives won't ever open on this thing. It doesn't make sense to replace one at this point, as I won't need this computer once I get mine. I have a copy of 2008 server and countless copies of Vista (I got more free as "promos" at launch time than anyone could ever possibly use) I could use, but hopefully I will have my own computer before I get this thing completely setup and re-formatted again.
The work laptop is actually somewhat new but it takes 15-30 minutes to boot and be usable and also has issues talking to the home PC due to the work domain+network config (long story) so in short, that really doesn't work too well for me.
At this point I do believe I have everything installed that I need, but there is probably some stupid configuration error somewhere. Perhaps something with user profiles or something fairly stupid.