Be sure the Windows Control Panel stops updating: sometimes it takes a bit of waiting before all entries shows up. JFK should be listed as Fsdreamteam JFK
If you still don't see it, you probably removed the uninstaller .exe from the FSX root folder OR the uninstaller registry key (a bugged registry cleaner program might have done that), in that case, the easiest solution is to install JFK V1 again, so it will reappear in the Windows Control Panel, then uninstall it so you can install V2.
If you get a warning about a missing area after you uninstall JFK V1, don't worry, it's not a real problem, just to in the Scenery Library and remove the area for JFK V1 that might have been left there.