Sometimes I just give up trying to fix an installation that's gone south.
I keep a working installation for each theater or war zipped up and ready to reinstall when needed. When I finally pull the plug on an installation, I just delete it and then unzip its replacement. Then it is not hard to add what little items I need to get back to where I was. I also keep weapons packs and scenery packs that have all the known working and functional items zipped up too. That way if I come up with a missing item error window, I can usually just dump a whole pack into the offending sim and solve the problem.
If you do delete, save your missions folder, GSL and whatever else you may want like your callsigns file and mdlname file if they were updated and you don't want to rebuild those.