For others who are interested, the detailed steps are:
1. Uninstall MyEclipse using the Uninstaller provided.
2. Uninstall Serena PVCS using Revo Uninstaller as it removes any leftover registry entries or folders. Make sure no directory exists under C;\Program Files\Serena.
3. Install MyEclipse 8.6.1 full installer. Open and make sure your projects load up correctly. Close the IDE.
4. Install Serena PVCS 8.4.0. During installation make sure that Eclipse 3.0 (Rich integration) is selected and in the next screen select C:\Program Files\Genuitec\MyEclipse-8.6 (depending on your install location).
5. Open PVCS and make sure your workspace and project directory load up as normal.
6. Open MyEclipse. Pulse notification will popup saying that PVCS dropins have been found and then IDE will show everything perfrectly.
Thanks,
Biju