Hello and welcome to the community @Lord_Piper,
I'll try to answer your questions in the best way I can.
Question1: Reputation, as a messure of how your charater is know in the game, could have good or bad repercussions related to different features: death, identity, etc. There are many mechanics that we don't know yet but it would be related with skill bonus. Anyways, in that page you can find all the related info about reputation.
Question 2 I have to make a break here. During Domain selection people is going to select their settlement, counties, duchies and kingdoms. There isn't any information related to what we are going to on the screen - family name, coat of arms, domain name, etc. It should be happening during Kingdoms of Elyria (pre-alpha experience).
During Land selection all the people who have got land are going to select their parcels of land in their settlements, so it belongs to the Exposition period and Launch.
Question 3: If you have 2 different accounts and you don't merge them, you can have 2 different duchies in both kingdoms. Other thing is if you are able to manage 2 duchies at the same time in different places. It's the same thing as having 2 account and play in different servers.