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This is a bug with Joomla! sometimes forgetting to copy files on update. It only happens in about 3% of updates, making it very hard to reproduce and solve. Believe me, all three people who understand how Joomla's extensions installer works under the hood, myself included, have tried repeatedly to no avail.

Let's see how to solve this, now.

First, extract Admin Tools' package to your computer. Inside you will find a lib_fof30.zip file. Extract this file. You will see a directory called fof having been extracted. Go inside it. Copy all of its files and folders to your site's libraries/fof30 directory.

Next up, delete the plugins/system/admintools folder.

Finally, log in to your site's backend. Install the Admin Tools package twice in a row without uninstalling it before or in between.

Sorry for the complicated approach but we are not allowed to provide our own installer, which wouldn't suffer from this issue, on pain of being banned from the Joomla! Extensions Directory. We know Joomla is broken when performing extension updates but we are forced to use it anyway :(

Remember that we did not completely uninstall Admin Tools in order to preserve the settings. Since the settings (web application firewall and component configuration) are preserved the wizard must NOT show and the download ID MUST be carried over. This is what you observe which is a good thing. Anything else would be a bug.

As for your other question: there are no absolute rules which apply to all sites. What is "good enough" for most sites is the settings you get after running the configuration wizard with its default options.

Finally, you mention something important:

shut down by repeated attempts to break in that overload the website host resources

What you describe here is a Denial of Service attack. You cannot fight it with software installed on your site by its very definition. The problem occurs because your server's operating system and web server are overwhelmed by the number of requests. That's long, long, LONG before Joomla and, by extent, Admin Tools have any chance to run. This tells you that you need to put something in front of your server. That something is a DoS mitigation service such as CloudFlare. These services monitor the incoming requests and if you seem to be under attack they act as a floodgate, keeping the flood of malicious requests from ever reaching your server.

Regarding your last post, did you touch anything in plugins/system/admintools?! You can't possibly be getting this message unless you have some really old files in there. Try removing that folder and install the Admin Tools package again. If that fixes your issue call your host and tell them to stop restoring arbitrary files on your site without your consent.

If you are back into your administrator don't touch anything.

Regarding the plugin, I already explained why it wouldn't work.

Here's the problem. You are not giving me the exact error message. If you would paste the EXACT error message I could be more specific.

If the message references FOFModel (F Oh F) then it's coming from Joomla! itself or a third party extension. Joomla! 3.2 and later include the old version of our FOF framework and it's currently used by Joomla! itself (for the Post-installation Messages component) as well as third party extensions. The most likely cause for this is that you didn't pay attention to my instructions and you copied the extracted "fof" folder of lib_fof30.zip into libraries/fof, not libraries/fof30 as I said. In this case you've broken Joomla!. The easy way to fix it is: delete the libraries/fof folder (AND ONLY THIS ONE!!!!); extract a Joomla! installation ZIP file locally; upload the extracted libraries/fof to your site's libraries folder.

If the message references F0FModel (F Zero F) then the problem is an outdated Admin Tools, Akeeba Backup or other VERY OLD Akeeba extension file on your site. Long story cut short, we had a private copy of our framework distributed with our extensions since Joomla! wouldn't update FOF fast enough. The private copy had the prefix F0F (F zero F) to prevent conflicts with Joomla's copy of FOF. However, we haven't been using it since May 2016, i.e. the last year. If you have a message about it you either have a woefully out of date file on your site or your host has screwed up the files on the site. Without the error message I have no idea which of the two is most likely.

If the message references anything else I have no idea without looking at the actual error message and the file it references.

Thus if you want me to help you I need you to copy and paste the exact error message, verbatim.

I am glad my educated guess helped :) With the screenshot I can see that indeed the referenced class is FOFModel (F-oh-F), not F0FModel (F-zero-F), as I suspected.

Just one last question: the Quick Setup wizard is now displayed when logging in to AdminTools. In the documentation it says that the Quick Setup Wizard button will not show up once it has been used. After the recent issues and changes, I'm not sure whether I should run it or not. Is there a way to check and make sure I don't run it twice?

Do you see the Quick Setup Wizard itself or the Quick Setup Wizard button? If you see the button, don't run the wizard. If you try to you'll get a big, red warning that doing so will reset your settings. That's why we don't want to do it. So, in this case there is nothing to do, stop reading my reply ;)

If, however, you see the Quick Setup Wizard page itself it'd seem that at some point you uninstalled Admin Tools which means that all your settings are gone. If you also get a red error message at the top of every backend page stating that Admin Tools is not configured yet then and only then go through with the Quick Setup Wizard.