So how does the stance meter work in story mode? Do you get to move your tracker around freely? Do you have to take checks on neutral?

We had this issue come up when a PC was selling some goods he found. Everyone seemed to note that, if you can be in a stance while bargaining, there's no reason why you wouldn't choose being Conservative. The logic being that with Reckless you can always roll a fatigue, but with Conservative you would roll a delay...which has no bearing in story mode to my knowledge.

I can't find a specific rules for it but the GM section is pretty clear that when there is some sort of conflict (social or combat) such as bargaining you should switch to encounter mode (ToA: PG 12). You can use a progress track to deal with the NPC merchant.

However you decide to do it, I would impose some consequence if they roll a delay. Maybe the merchant doesn't feel that like haggling all day so he refuses to sell it to them. Or perhaps the delay is so long the shop closes and he decides to go home for lunch.

Story mode has plenty of ways to utilize delay. The negotiations take longer ... this could lead to the players being late, missing certain story events, not being able to buy as much stuff as they want, etc. It could also represent a delay for the vendor to provide the item(s) in question.

As for stances, I tell my players if they want to use stance dice in Story mode, they have to roleplay it. If they roleplay being conservative and calculating, I'll let them use a 1x Conservative Stance. If they are angry and headstrong, I'll let them use a 1x Reckless. If they want more, then I enter a Social Encounter, where they start at neutral and have to work their way up. You could always just charge them Stress for choosing a particular stance position in Story mode. Stress doesn't recover automatically, so it might stick around for a bit.

I give my players one favoured stance die for free in story mode, as that is their natural way of doing stuff. If they want a different stance then they have to justify it by the situation and the roleplaying.