The underwear you use, depends a bit on your other layers. If you like running with tights that are made for cold weather, you don’t need long underwear underneath. If you are using thin tights only, it makes sense to have some long underwear.
If you will dress like a hiker – which is what I did when I did the recce – it makes sense to have long john’s just in case it’s really cold. Even if you end up not using them for the race, you may find them useful for camp life.
As to what material and just how thick, that’s a matter of personal preference. I would say you don’t want it too thick because otherwise you will quickly work up a sweat on the steep uphills. Synthetic materials will breathe better than merino wool but of course merino wool will help against odor … There are also good products that blend both.
I definitely always have one spare base layers with me because even if I don’t wear much, by the time I reach a mountain pass I will have a wet shirt. Then it’s nice to be able to change. That spare base layer may of course also be a running shirt and not underwear.
It obviously makes sense to be able to wear a fresh pair of socks every day.
The one thing that may differ from what you normally do, I recommend you take at least one pair of thin waterproof socks from DexShell or SealSkinz. You may get your regular socks wet and on a cold day or when you are high up, your feet could get cold. Waterproos socks will shield you against the wetness of your shoes and retain body heat. So, these waterproof socks should be in your backpack. Just in case.