How can I find all the changes I've made to my system via "defaults write"? Over time, I've made many tweaks to my OS using defaults write, for example:

defaults write NSGlobalDomain KeyRepeat -int 0
defaults write NSGlobalDomain AppleShowScrollBars -string "Always"


and so on.

How can I generate a list of all the non-factory settings I've overridden?
It's not possible to distinguish changes made by you with defaults versus changing the setting using the GUI equivalent preference if one exists, since both perform writes to the property list files in the same way.

Theoretically, the default value shouldn't be written to preference files. Therefore, the only values in ~/Library/Preferences property list files should be ones overridden by you. You will have to investigate these files for the preferences you're using.

Create a new user account and open the software you use without making any changes. Diff the contents of ~/Library/Preferences from this user account with your normal user account, such as with Kaleidoscope, to identify changes made to preferences.