After quite a bit of research and consulting with others that have experience with this type of upgrade, here's the consensus.
Yes, Microsoft not only suggests, but apparently will walk you through this type of upgrade. However, it rarely works without issues. Some quite severe. It is recommended that you Backup your data and do a fresh install of the Operating System. From the standpoint of Malware (the focus of this part of the board), your machine logs indicate that your machine is clean. Last, we do have an Operating System section of our board here. If you'd like to get a second opinion, I think that would be wise on your part.
If you have any further questions, let me know. Also, please post back so that I know you've read this. Thanks!