Does blocking with a two handed weapon mitigate arrow, bolt or spell damage on any level?

It should though not as well as with a shield. And you do have assign perks for those in the block skill tree.

No...right side of block tree works with weapons, as well as block runner. Arrow and spell perks do not work with weapons

NO. If you can block an arrow or spell with your sword then you are a Jedi and should post on the Star Wars forum