I think you might have the most success with a completely clean install. That will give you the opportunity to set up any special partitioning you may desire. Remember: It is always a good idea to make a backup copy of your most-crucial files.
I use a flash drive to copy a few documents, pictures, and music. I performed a clean install of Mint 5 - not saving the /home folder. With everything "Minty fresh," I copied what I wanted back in the right places, then tweaked a few settings. I was up to speed in under an hour. Your needs are different, but what you do at this important juncture will be the solid foundation for your continued Mint happiness. Good luck, and have fun!