I'm not playing the game, but I have a suggestion: this sort of game really needs a formula based pricing for items instead of just made up numbers. It's the easiest way to get balance on things.
For example, you might have an item chain valued like this (completely made up for an example):
Production time is valued at $1 per unit (unit being second or minute or whatever). This one would need to be set based on how profitable you want the game to be, and could be adjusted for the cost of the factory or store by making the higher priced factories more productive (IE, million dollar plant might produce 10 units of production in a minute, while 100k farm might produce 1 unit of production in a minute), and this value minus what your factory fixed costs are would effectively be the processing profit on the item.
Water takes 1 unit of time to make and no ingredients. Valued at a base of $1.
Wheat takes 1 unit of water and 2 units of time to make. Valued at a base of $3 ($2 + $1 for the water).
Flour takes 1 unit of wheat and 1 unit of time to make. Valued at a base of $4 ($1 + $3 for the wheat).
Porridge takes 1 unit of wheat 1 unit of water and 5 units of time to make. Valued at a base of $10 ($5 + $1 for water and $4 for wheat).
And so on. And selling them would have a demand model in dollars, with a similar profit model as manufacturing - selling flour in a store for $8 might take 4 units of sales time, while selling a porridge for $20 would be 10 units of sales time. Now obviously it's more complex than this, and you have demand models and such that need to be decently complex and you have bonuses to production and to sales based on scale and batch size. But if it's all based off this system with good demand equations and no magic bonuses for high value items, you would have a system where every item is theoretically the same profitability. You wouldn't need bonuses for more complex or expensive items or the like, as those items would naturally get bonuses due to supply and demand - more people would produce easier to produce stuff (at least at first) and the first to make the more complex products might enjoy a relative monopoly for a time.
This sort of pricing model for everything would immediately bring all products into balance, and the profitability of products would solely depend on the market forces - ie, other players and how they're behaving. I would play a game like that, as then it's less about exploiting bugs and/or quirks in the system and more about exploiting opportunities in the market.