I went forward with the Server 2003 R2 install and then added VMWare Server 2.0. Trixbox installed very easily and quickly and I added chan-sccp-b using these instructions. It all went together very well and once I remembered all the places my old config files had old IP's (I copied over the sccp configs) I managed to get a phone to connect and call to an IAX2 softphone.
However, I can't get the trunk to the router to work. I'm getting a 488 error in the debug which seems to suggest a codec mismatch. Both sides seem to have correct dialplans as they try to call through but all I get is a reorder tone. The Cisco router really only supports g711 in the current configuration. Could it be that the Trixbox isn't enabled for that? If that's not the problem, I'm not sure what is, yet.