For what it's worth I felt like you were doing fine, the only thing I personally would've maybe tried to do more (and this has nothing to do with your method and everything to do with the fact I have Worldbuilding Disease) is point players in more concrete directions and give more OOC knowledge of what's available by using the Setting itself. For instance, a descriptive blurb of each Environment with a few lists of the basic monsters that might be encountered there, the basic resources that are there, and any potential challenges Players might face there---for instance, maybe the Swamp has a chance for something like: "You get mired in the mud, adding 1 hour to your travel time," which means Players might find themselves caught outside the village at night, or not being able to accomplish all their plans that day and having to adjust. You could still leave room for things to be discovered in the "deeper" areas of each biome, or just outright omit certain things from the list (complete with a ??? mark to whet the Player's appetite for curiosity).
Maybe also a list for the Village itself containing not only descriptive info, but how long certain tasks will take. The safer and more developed the Village became, the less upkeep might be needed---right now "House Repair" would take 3 or 4 hours to advance the house from "Ruined" to "Abandoned," and 2 or 3 more to advance it from "Abandoned" to "Fixer-Upper." So Players could structure their activities around what they want to accomplish, but once the Village itself is stable they're literally given more time to do other things, subtly pushing them towards unexplored regions of the map.
The flaw in that method is that it sometimes feels railroady or like it takes the "discovery" out of things, which for a Slice of Life, cozy farm RP like this one is vital. You're not aiming to push Players along with a plot, you want people to play out their roles and be chill, and that's fine too. Aiming for something free-form and relaxing can be better than something rigid and structured, it all just depends on Players and GMs and communication.
A piece of GMing advice that has helped me a great deal whenever I think "Okay, my Players are going to be in THIS Hub Area for a while, what do I need?" or "I want my Players to have reasons to leave the starting block and go Here, There, and Over Yonder; how do I motivate them?" is this:
"Every Scene/Session, give Players choices to: Go Cool Places; Talk to Interesting NPCs; Learn New Info; Fight something; and/or Get a Reward. All choices should achieve Plot Progress somehow!"
For a non-action based RP, you could replace "Fight Something" with "Complete a Challenge." Maybe you tell Players "A powerful storm is blowing in on the horizon! You have 1 hour to prepare!" and now Yingmei has to chase down all her chickens and Akitsugu has to help Darryl nail everybody's windows shut. You've actually already accomplished most of the stuff on the list, in my opinion---Cool Places, with Rewards in the form of Resources; Interesting NPCs, who can tell the Players New Info; and the Plot Progress in this context is the progression of the Village itself being rebuilt.
Don't be so hard on yourself, I enjoyed this RP a lot and didn't really think anything was going wrong at all. If you felt anxious or worried, or like people weren't being active enough, it's okay to communicate those things.