Might i suggest if its supposed to span 3 ingame years to split it in to 3 parts. That way you could focus on doing year 1 then take a break or do a mini project in between before returning to do year 2. It should help stop from burn out too. It could also help make the story clearer for you to write, having an over arching plot over the whole 3 years but each year itw own contained plot that builds up on top of each other.