I know you can pretty much play this without hassle on Windows 10 installing some fanmade patches, but those patches usually come with balance changes and shit like that thus, bad for speedrunning.

What's the best way to run this as "vanilla" as possible on modern OS?

AndrewFord may have a better solution, but my solution was to run the game in a virtual machine. It's fairly convoluted but you get the benefit of windowed mode (without losing an arm) and the equivalent of save states, though for this game isn't as necessary.

Is there a guide or something similar to setup a basic VM to run this game?

I found VMware to be fairly intuitive. I recommend a CD or ISO of Windows XP; there's various places you can obtain one. It guides you through your first installation and shows you how to enter/exit control of the virtual machine. Besides that it's like installing windows on a new computer. There's some tweaks I can recommend once you have everything installed and running.

But if you do get too confused along the way I can help out.