I'm not sure you will like to hear this but here goes…
This is Mac it looks like you have migrated older data onto this machine, probably via Setup Assistant. You can clearly see that many older applications, plugins & junk have been installed. Some of these may be harmless, disabled or not active, however occasionally one of these older apps will conflict & can cause the issues you are seeing. Old applications also have known security vulnerabilities that can expose your machine to attack, if it is installed & used it needs to be up to date.
Have you considered that it would be better to start with a fresh copy of OS X, that way you won't need to 'peck away' at what appears to be years of cruft that was apparently installed on another Mac. For example Soundflower is installed & unused (the kernel extension is unloaded), that version is from around 2009, when El Capitan was just a big rock. Your /etc/hosts file is modified, it makes me wonder if this is deliberate or left over from some malware or other 'hack'.
I understand that you probably want all your old user files, those can be moved over without the extra junk & for the most part those files will not break the entire system.
Here is how I would approach it…
- Backup to an external disk, ensure it is a bootable copy (make several copies if you are paranoid, one backup is never enough).
- Boot to recovery mode (cmd+r at startup)
- Erase the internal disk in Disk Utility, quit to go back to the installer.
- Install OS X (DO NOT MIGRATE ANYTHING YET).
- Create a new admin user via the assistant, use a different name to your old account.
- Login, open /Applications/Utilities/Migration Assistant, connect the external HD with the old backup.
- Navigate through the assistant & select the option to migrate your user data. Do not migrate Applications, other files & settings.
- Finally install all the Applications you actually use, getting the current version from the developers site (or the App Store).
Your user account should be the same as you left it when you next login, so be aware that the login items may need cleanup. System Preferences > Users & Groups, login items tab is where you edit them. There will be cruft in your user account, however that is less harmful to the entire system.
The Applications option in Setup/ Migration Assistant will import all supporting files for apps, this inflates your backups & can cause issues like the ones you describe here.
If you want you can promote the migrated account to an admin & delete the one you created at setup but it is safer to use a non admin account for day to day use if you can stand the occasional dialogs.
Ask if you help to want to pursue this option.