Welcome to my project for the semester Mike
You won't be able to use system III Mike as it relates to the rotation of the actual planet and is measured using radio wave or magnetic field fluctuations. Can you be a bit more specific on what you are trying to achieve? There are a number of ways of measuring features against time/date/longitude.
I don't have it with me atm, but when I get home I'll post a grid you can use to measure features (GRS, spots etc) against the Central Meridian and other longitude. Once you have a time of crossing the CM then you use the conversion tables in Astonomy 2006 to convert to Longitude.
I've been using J2 but I'm certainly going to have a good hard look at WinJupos. Thanks for the link.