For full version upgrades I normally uninstall Domino, and install the new version, ensuring that I'm pointing the setup files at the existing Domino application and data directories.
I also suggest that you set the Domino windows service to Manual AFTER running the upgrade, prior to rebooting the machine. I've seen systems never come up after upgrade after this, and it's such a pain to fix. Set the service to auto after the first reboot.