If you get a freeze and/or a CTD after the Fly Now screen, it doesn't have anything to do with anything related to FSDT because, at that point, the needed modules were already loaded so, if they were affected by problems to your config (like antivirus, etc), it would be apparent on the initial FSX splash screen, not after the Fly Now screen.
The problem must be something else, the fact that happened after KJFK installation is probably coincidental.
The obvious test is, of course, uninstalling KFJK using the proper Uninstaller on the Windows Control Panel, and replying YES to the question about removing the Addon Manager AND the Couatl Scripting engine. After this, you'll be in the exact same situation as if KJFK was never installed.