Have you tried syncing your chrome to an account, and doing a wipe/fresh install? Perhaps the sync data is bad and it might be good to get a fresh sync going on a new account.
As you stated, the culprit was likely the experimental settings in about:flags which makes sense. Hard to always see the far-reaching impact changes there might have. Odd that it affected all extensions though.
Yes, but it depends on how they store their settings—there are (too?) many.
Cookies
If the extension stores its settings in a cookie, then you will need to find and delete the relevant cookies from chrome://chrome/settings/cookies (you can delete all cookies with chrome://chrome/settings/clearBrowserData if you don't use them in general).
Local Storage
If the extension stores its settings in local-storage, then you will need to navigate to the Local Storage directory in your UserData folder and delete the relevant data. For example:
%userprofile%\AppData\Local\Google\Chrome\User Data\Default\Local Storage
If you only want to reset some extensions, you can cross-reference the filenames with the extension(s) in question by selecting the Developer mode option in the chrome://extensions to see the GUID (e.g., mgijmajocgfcbeboacabfgobmjgjcoja = Google Dictionary, so delete chrome-extension_mgijmajocgfcbeboacabfgobmjgjcoja_0.localstorage)
Databases
Extensions can also store their data in the Databases directory:
%userprofile%\AppData\Local\Google\Chrome\User Data\Default\Databases
Again, delete the relevant folder(s).
Post-reset
Finally, restart Chrome and the extension(s) should be reset to their default settings. Depending on the extension(s), they may or may not pop up their configuration page and ask you to configure them for the "first time".
Best Answer
Mouse over the search bar on the right side next to the bookmark star. Once you see the re-size arrow indicating you can resize the window drag it to the left. They will cause your search window to be smaller and will enable your extensions to appear in the top bar.