"The only problem I still have is when I place a lot of buildings and have them all be crafting things at the same time. Say I build 1000 furnaces and they are all making different items. I still get a few hundred item drops on the floor that start to lag the game a bit (drops about 10-15 fps, so it's still very much playable). I am going to experiment some more on how to optimize this as well!"
You probably solved this issue already but a common way games handle it is to have local storage in the production item. Eg Factorio. These storage can fill up but you could set the max high. Mousing over the storage bin could pick it up until you get the upgrade that automatically moves the item to your inventory. That perk could also teleport the item instead of showing an animation to help reduce lag.
You could also have storage collector boxes that are generic that just suck the items out of the furnaces every n seconds. These could have a radius effect just like the generators. You could then periodically go to the storage as a player and grab what you wanted.
When selling giant piles of things it seems like a sound is generated for each thing. This causes some crazy sounds and in the demo it actually causes the music to stop playing.
ps: I LOVE this game :)