To me it seems that most likely the turaga have some sort of mental link with a matoran production facility somewhere in the inner workings of the MN robot. When a matoran died, a turaga would get a message from the dead matoran's body (mentally) telling them that a matoran needed to be produced. They would not be aware of this though as it would take place in a part of their mind they do not use (like how we humans only use 10% of our brains). Then the turaga would send another message to the matoran production facility, telling it a matoran was needed. How the matoran are produced is explained here. I think the organic material how ever would be produced in large vats or tubes. Some of this organic material would be put through extremely different conditions in order to differentiate it from the others (this process would be completely randomized). Then a machine with advanced AI would create an AI/personality for the matoran. The machine would examine the differences from a control "matoran brain" and from that information create the AI. Now the newly created AI would be examined even further to decide what element/gender suited it best. Once done the matoran's robotic skeletal frame would be made along with bodily organic material. Finally the matoran's brain would be added and a mask sealed on the head. Now the finished, unawakened matoran would be sent through chutes to its destination. Once the matoran arrived it would awake and have a mental not within its head telling it where to go and who it was.Hope you like my theory