Can I still use my AES for this update
No, you will probably have to wait for an updated AES support. Since we haven't changed the actual jetways models, there's nothing needed on our side of the things.
also will the extra autogen give issues with Ground Enviroments, Ultimate Terrain or other
You can always try, that's why we have a Trial version for.
If I prefere V.1 to the new version can I re-install this older version.
Obviously yes, that's why we have uninstallers and installers for...
Can the afcad be changed using ADEX, if so what is the best way so that I do not get issues.
I don't foresee any specific issues, as long you don't rename the file and/or start changing parking names, because that would screw up GSX, which has been carefully customized for the supplied AFCAD and if a one with a different name is found, the GSX customization will turn off, and the airport will revert to a default GSX behaviour, note that GSX is used to create Docking Systems at JFK, so GSX without the proper GSX customization, there will be no docking system too.
Basically, consider GSX to be a part of the scenery...
If you just change airline codes and add new parkings, there will be no issues. But please keep in mind that, whenever you run any update that requires running the Addon Manager stand-alone installer (a major GSX update) all your AFCAD will be overwritten with the FSDT ones. A backup will obviously be made, so you won't lose your changes, but you'll have to replace files anyway.