Here is another update for you guys.
I restored the week old Time Machine Back-up, from before High Sierra was installed, that resulted in a perfectly working machine, but with outdated data. After making sure everything worked as it should, I went to the App Store and downloaded High Sierra again and installed it. First thing I tried was installing the drivers again, and three guesses what happened. System Extension was Blocked, no Allow button, back to square #1. Played around with it a bit and it was exactly the same, not only the extension problem, but Time Machine couldn't connect to my Time Capsule and DMGs started making Finder Crash again.
So I was left with the last option, a clean install 😢
Which is what I did, I made a bootable USB drive on my MacBook, since that didn't work on my iMac, it kept crashing on downloading the installer or putting it to USB. So MacBook to the rescue. I rebooted the iMac into recovery, wiped the Fusion drive and installed MacOS from the USB disk. Which resulted in a perfectly smooth and operational MacOS High Sierra installation. First thing I did was get my drivers, installed them, got the System Extension Blocked message, headed to Security and Privacy and lo and behold, there was an Allow button! I clicked it, rebooted my machine like the installer wanted and my 3D mouse worked like a charm 🙂
Messed around with DMGs a bit, seemed to work fine, so I connected the USB drive with my latest Back-up (after HS install) and started putting all my files back manually, luckily that's an easy process since you just get your file structure in the back-up, so it's just a matter of dragging and dropping files back to where they should go.
Again, it's 1TB so that took hours, but hey, I had everything back in working condition 🙂
Until last night. I was mostly done putting everything back, my files are back on there, the smaller apps were moved or redownloaded, just had a few more to go when I noticed an MacOS update on my macbook. So I headed over to the App Store on the iMac, no update. Clicked the tab again "Error, could not connect..." Euhm... Opened Safari... back screen. Restarted Safari, black screen. No sites opened. Opened Chrome, no issues, worked fine.
Mail worked, Photo's didn't sync. iTunes Store works fine, Maps works, App Store browsing works, just not updates or actually downloading apps. And Safari does absolutely nothing. Page starts to load, blue bar starts running, stops. Page stays white, no error's noting, just stay like that.
I made a new test user account, and there everything works fine, so something in my user seems messed up, but I did nothing that could have messed it up. I moved some files, installed some often used and trusted apps. How the heck did that mess up Safari from working and some Apple Apps from connecting?
So I "fixed" my original problem by nuking it. But then a new issue posed up. I'm reinstalling MacOS over it again, which will 99% not do anything, but hey, it's worth a try before I call Apple again. I'm getting really tired of this. I haven't been able to use my iMac in over a week now :/
So to everyone with the "System extension blocked" issue, it seems like a clean install is the only way to "fix" it. I hope no one else encounters other issues along the way, though.