I would suggest an new feature where you can limit farming plots production. E.g Clicking on your Pumpkin field should have a imput window where you can define the amount of stored pumkins. E.G 50. When your farmer realize there is 50 Pumpkins in storage he/she will stop harvesting pumpkin. This will reduce the lag caused by items as well as address the multiple food baskets standing everwhere. For Chicken coups and sheep just add a flag in the middle of the field with the same option, but with a setting for both the pruduct (e.g. eggs) and the animals. When the animals reach over this number one will be slaughtred.
E.g. Pen Size 19
You could set the harvest ammount to 18
When a 19th animal is born an adult will be slaughtered.
On disease - Allow animals to get diseases. For example a sheep can get contract FootnMouth(animal limps around with its foot in it’s mouth) 
Disease. Your herbalist must keep not only human cures but also animal potions is stock.
The diseases could have funny names and results. E.G. Bloaty Disease causes your sheep to first bloat and them float away with the wind or explode if no cure is available. Also your healer could accidentally administer the wrong antidode and cause somethin else to happen to the animal. This makes for all sorts of fun.
