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The tavern entrance issue shouldn't matter where the exit is. The solution is simple, add a turn up before the move forward. Or better yet, make it so that you need to be facing up to trigger the event (so that the player doesn't accidentally trigger it).

For your farming system, use a common event and variables/switches to call the common event in a way that allows you to manipulate each plot's variables individually. That way, you edit one common event and it affects all the plots at the same time.  This is easier with a script call as script calls are a bit more flexible.

You can do choices as a script call instead:

Example script call 1 (initialize the choices)

//Load Variable with choices (in-game variable)
 
$gameVariables.setValue(101,
[
"Lily Weed", "Rabbit Seed", "Star Bloom",
"Kingsglaive", "Meadow Flower", "Toadstool",
"Vine Grass", "Cinnamon Blade", "Tragic Hero",
"Queens Seat", "Pig Feed", "Glow Bell",
"Lotus Bloom", "Nightshade", 
"Spider Lily", "Cleric Bane",
"Cancel"
]);

Script Call 2

// Set Message Choices. (101 = array variable, 0 = default choice
 
//-1 = disallow cancel.
$gameMessage.setChoices($gameVariables.value(101), 0, -1);
$gameMessage.setChoiceBackground(0);
$gameMessage.setChoicePositionType(2);
// Record Outcome in Variable (102 in this case).
$gameMessage.setChoiceCallback(n => {
$gameVariables.setValue(102, n);
});

This way you get a choice menu you can scroll through like this (notice the arrows showing that there are more options to pick):

Once you've selected the option, you can then load that value from the choice variable into the plot's variable.  There are also potentially ways to show how many of a seed exist and to disable options if you don't have enough seeds or even potentially dynamically create entries based on your inventory seeds.

There are other ways to do this, such as changing the function so that it shows the options side by side when there are more than 8 options and having it scroll sideways instead of vertically, but that would require a bit of editing to do. (I've also showed another way to do it in my tips and tricks dev stream (August 17th's stream))

Path finding is honestly very easy if you know what you are trying to do. If player is facing up, you know the player is below. If you have members, you assume all possible member positions are taken and adjust the script accordingly. What you should do though is load the player's x,y values (easier than getting the event's x,y values in this case) and directional facing. Using that, you can figure out both the player's position and the event position. Then based on that, you can have several move paths that move the event to a set location and then it is a simple move path from there (or you can teleport once off-screen).

Or, if you have to teleport, do a fade out, teleport, then fade in. (A no wait flash can also work, just be careful with timing).

Like I said, I liked the ideas. A lot of potentially great features that you could use to make a farming sim or alchemy sim. You just need to be careful with your story so it doesn't feel out of place. I can't tell if you meant Dragon or Dragoon (two different things) and other problems with the story exist. 

One thing you could do is to actually set a pacing so that the player is going about their daily lives and then one day, you hear a crash on your way back to the house. This way, you've set up what is 'normal' (this is more of a horror/tragedy story technique, but it can work in other situations as well). You can also slowly feed your player information this way. For example, you might go and visit your father's grave (with or without your mother) one day a month to keep it clean and on the second day, it happens to be that day.

There, the player could learn at least a little of what happened with your father. Once you assist the ally and discover the truth about them, you might not help them right away, but instead have the ally leave. You might then later see the ally collapsed on the road again and out of compassion, maybe hide them in the alchemy area (to avoid discovery by the mother) and care for them in secret, sneaking food off and such. Just until they recover. 

Then, while taking care of them, maybe discover some information that makes your character want to help them beyond recovery. This would then give your character a solid reason for wanting to help. Maybe the mother could notice and observe in secret (could show a shadow moving in a window one day to show the player if desired) and possibly even soften her heart when she learns that not all of the group are bad. This would drive character development for the mother.

Now, this would be a lot of work, setting it up so that the characters act differently each day (I mean the NPCs) or at least having a reasonable explanation of why they might always be the same. As an example, you might have a 5 day week and 4 week months (20 days). Each week, you might have 1 day where one of the shopkeepers will be home resting instead.  (Since this would take time though, you might skip it and just have a routine that makes sense to repeat).

Instead of having a long main questline where you leave into the open world, you can have little side quests from various NPCs, some might even repeat every x days (for example, maybe a shopkeeper tasks you with making supplies to sell because they are running low just before their restock day. They might not sell that item until they restock and ask you to provide you with a few to sell to others (not back to you)). This would make it have a more sim feel.

Speaking of quests, you have a lot of default/plugin tutorial quests that you don't want in the actual game.