I spent some time on this as well. It's rather complex, but I've mostly come to the following conclusion: time wise, the basic items are more profitable to produce. Nails is a very good example of this.
I'm at level 32 and the most complex item I can build to maximize profits is the watch. This is because it doesn't need materials produced by the other shops.
The other issue is that the basic items are produced fairly quickly, so you need to keep restocking you shops constantly. Things start getting complex when you can't play the game for long periods of time.
