I just tried uninstalling all sceneries from FSDT and removed bglmanx.dll and couatl.exe etc... EVERYTHING removed!
Then I installed KJFK OFFLINE, and forced the installer to use the 2.0.0.2081 of couatl.exe - It then WORKED!!!
Buildings and everything was there, in JFK... and Couatl powered was visible in Addon Menu!
When installing KSFO v2.0 everything reverted back to the original problems... I tried copying version 2.0.0.2081 and overwriting the SFO version, but the problems remains... Buidlings was missing (both in KJFK and KSFO), and couatl powered was missing too from Addon Menu!
This is probably to be expected, since since you said, that the version 2.0 of KSFO, won't work with older versions...
The problems emerges, when installing the new version of SFO, or downloading the new version of couatl.exe from either the addon-manager setup, or installing any new scenery using the engine.
The version downloaded, I believe, is version 2.0.0.2141 - so far, I've only managed to get couatl.exe to work with OFFLINE installation of KJFK ... i.e version 2.0.0.2081 - WITHOUT KSFO v2.0 installed!
It is then probably important to mention, that couatl.exe IS running in the Task Manager throughout the whole process!
I don't know if the above means anything, but I'd thought I'd share the information!