10.13 upgrade problems (security issues?)

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I've successfully upgraded a 10.12 drive to 10.13 (I believe it's 10.13.6) so I continued by downloading and applying a security update and that's when I started getting problems. Luckily this is on an SSD for testing, not my main boot drive (10.11), so it's not critical, but I would eventually like to upgrade my regular boot drive, so I'd like to sort this out.
I'm on a Mac Pro 5,1 (mid-2010).

Apps like Little snitch were disabled with an alert telling me to go to the Security & Privacy system preference. Likewise with other stuff installed (a SATA PCIe card driver, Wacom tablet driver and other stuff I'm not sure what is) there apparently was a security issue or something. I took several scrrenshots, but now I can't even access the 10.13 drive.
Anyway I gave access to those apps (in the security system pref) and rebooted but kept getting the same error messages. I probably rebooted 5 or 6 times with the following screen coming up in the boot process:

I can't remember all the details around all of this, but the 10.13 drive isn't available in the Startup disk system preference, neither is the drive shown in the 10.11 Finder desktop as it did when it had 10.12 on it (or else I could have accessed the screenshots made there).
So I have to hold down ALT while rebooting in order to choose the startup drive. Then the progress bar pops up which makes it appear like everything is OK, but it never ends, and the fan speeds up (I've waited 20 minutes or so until I forced the power off by holding the power button for several seconds).

And in Disk Utility (from within 10.11) I can see the actual drive, but there's no partition, or at least Disk Utility says so (even though there's something there since I get the disk name to choose to boot from when holding in ALT upon booting and it does then boot into something -hence the progress bar in the above photo).

Does anyone recognize these problems, and know what's going on and how to solve them?

 

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UPDATE: After hours of trying to fix this I finally have a working 10.13 setup!
After multiple failed attempts I managed to get into recovery mode (CMD-R while booting) -the key was to keep holding down those keys all the way until I would actually get into recovery mode and see the "Install MacOS again" option which I used.

However, I had to go through this a grand total of three times! Each time I would be greeted with this (no, this is really how it looked (except the alerts being cascaded on top of each other):

Then I would start with the problems concerning Little Snitch, go to the Security & Privacy system preferences where I would click on the "Allow" button as seen here, followed by rebooting the machine.

As far as I remember I went through multiple instances of that white "Your computer restarted because of a problem" screen as shown in my previous post.

Well, Little Snitch started working again this time, so I must have done something right (or been plain lucky), but I kept getting other similar error messages telling me to go to the Privacy & Security preferences again, now with a long list of names (for some reason only showing 3-4 names at once). This time I didn't tick any of those boxes because I think that's what gave me the deep issues which prevented being able to boot into 10.13 at all).

So next I applied the 10.13 security updates (I think there were two) and again received some alerts:

I think they've gone away since then, but if I'm not mistaken some functionality has been removed (all those tick-boxes; "Legacy developer: Canon" etc.). Are they so called KEXT files (kernel extensions) meaning "drivers" as Windows people call them? What do I do to remedy the situation and why have I run into all these problems in the first place?

UPDATE: a little thought..... I read in another thread that when upgrading to 10.13 on an SSD you've have the file system automatically converted from HFS to APFS, and this could be problematic. Maybe that's the reasons for all the above problems. Any thoughts on this?

Another thought is that the SSD which has now been upgraded to 10.13 is mounted in the lower optical drive bay of my Mac Pro 5,1 and is attached to a cheap SIL3132 eSATA PCIe card, and "Silicon image" (as seen in one of the software items listed in the security preference pane as being blocked) might be the reason. I don't know what I'm able to boot into 10.13 now, as the driver is apparently blocked, and I also don't know if there's a 10.13 compatible driver for it (the card's website seems to have changed ownership and there's no longer any mention of this card).

UPDATE 2: Success! ? ? ?
I don't know what the cause of all the above problems were, but since this was all on a test-SSD I went ahead and reformatted the drive, installed 10.12 from scratch, upgraded to 10.13 (from the command line, to avoid it converting the file system to APFS) and applied the security updates. It went fine this time, so this is probably the way to go.
Perhaps I just had some messy KEXTs or something.
And the SIL3132 PCIe SATA-II card (attached to one of my 2.5" SSDs) works fine without a driver at all! The driver is probably just for adding RAID support.