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Hmm, that pretty weak but you will manage. Plex recommend around 2000 passmark points for encoding one HD stream. Opteron seems to have 1400 points, so if you have two it should be alright. Also, streams don't always have to be encoded. What can you do with this server depends only on how much you want to learn. I would say start with a hypervisor, set up media server and maybe file server in VMs, learn a little bit of linux in the process

Free server, awesome! You should definitely visit r/homelab on reddit. There are many tips for what you want to achieve there. Second thing, if that server has enough RAM and CPU power then the best course is to virtualize everything. Keeping growing projects in one OS is just bad. You can do that in Windows but Hyper-V is not the best hypervisor. If you want some help you can always PM me

Everything in this kind of server is designed to run under constant high airflow. The duct and the noise are there for a reason. I would say you are starving RAM or some other component out of air. It can be something else tho, definitely try memtest.