The usual reasons for CFS3 to crash is either a mismatch in the GSL or several versions of the gsl being found. Or it could be something invalid in the way you have set up your new airbases.
I would suggest removing all your additional airbases using scenedb. If it then works without crashing add the new airbases back in one at a time and see if one particular one is causing the crashing.
Do you mean you tried removing all the extra scenery and it still crashed?
If so then manually restore the backups that should be in scenedbbackup (they will need to be renamed back to the appropriate extensions) and see if it works then. If it still crashes then there is something else wrong with your CFS3 setup