Ok, this is extremely frustrating. I did a clean install and then used Migration Assistant to get my old system back. Everything worked flawlessly. Wifi/Bluetooth back to normal, boot time around 10sec and both NVME drives were showing.
And then, something happened. I was stupid and dismissed the message too fast, so I actually don't really know what exactly happened but I'll try to explain it as good as I can.
About two hours into using the computer, macOS gives me a message that some "add-ons" have been updated and that I need to restart to use them. I'm writing "add-ons" because I use the OS in Swedish and I think the direct translation would be "extensions", but I'm pretty sure the message did not refer to kexts. Then a window opens with a long list of items that almost all had a name with "- unidentified" at the end of it. The list very much resembled one of the lists under Privacy and Security in System Preferences, with tick/slide boxes to the right of each item. I now CANNOT find where this list is now though, it's nowhere in System Preferences as far as I can tell.
I didn't think much of it and clicked restart, and boom - all the problems I've been talking about previously in the thread was back. Second NVME drive not showing, boot taking 4 min and bluetooth/wifi not working properly. The bluetooth problem literally started while I was typing, killing the keyboard connection.
This is beyond frustrating and I'm sorry for my stupidity to just click away the message before actually checking what was going on. Ofc, I can just do a fresh install again, and once that message and list shows up again I'll take screen shots. But maybe
@CaseySJ or someone else might be able to figure out what I'm talking about and correct whatever happened, to spare me another 3-4 hours of work.
Thanks!