I have clean installed KJFK 2 into P3D V2.1 but when I try to install the update to KJFK 2.1 I get the message that I have to install KJFK first - which I've already done...
The 2.1 update can only used to update a JFK V2.0, which is not available anymore. If you installed JFK V2 using a recent installer, it's already a 2.1 version, which is of course can be confirmed by checking the version of the installer.
The general rule with our products is: all full installers you find on our site on any given date, are always the very latest versions available on that date.