Some of these issues are ones that were experienced and solved by the big IRC networks. They used different methods - nick registration and authentication via a bot, for instance.
The source for many of those is available. Why not see how others solved the problems? A brief look at the Charybdis IRCd source (at least the Freenode version) shows capabilities for limiting channel creation to authenticated users and what looks like built-in ChanServ and NickServ.
In any event, you may be worrying over nothing. I ran a friends-only IRC server back in the day and didn’t have issues with impersonation. I rarely saw any unknown users and it was easy to detect them because they weren’t part of my circle of friends. We had a couple bots that logged the channel and provided various services - it wouldn’t be hard to have one enforce security.
I’ve got a different Supermicro board. I’ve noticed that it’s extremely sensitive to SATA issues - if something isn’t just right it doesn’t boot or gets all kinds of wonky. A flaky cable is enough to cause issues.
I assume you’ve tried it with nothing but CPU, RAM, and video, but if not give it a shot.