The next step is to look at the circuit board and manually generate a set of schematics. It is possible to see the little wire traces that show the connections between things, and you can see where the components touch the traces making a connection. To begin with, you do not need to understand anything about why certain components are connected to other components, you only need to know how they are connected.
Armed with a pencil, some scratch paper, a jewelers loupe, and a multimeter, I traced the wiring between most of the components. From that, I generated a set of paper schematics for the Aprilia fuel injection computer, or ECU. The scribbled paper notes were then transcribed into schematic diagrams using Cadsoft Eagle.
Yes, it took a long time. There were many hours spent up in the loft after the kids went to bed.
Once the schematics were in Eagle, I would stare at them trying to deduce what they were doing. Sometimes, it was really easy, like for the coil and injector drivers. Other times, like for the MAP sensor circuitry, it was a lot more difficult and I had to read some books to figure out what I think was going on there.
That brings up a point: these circuit diagrams are neither complete, nor guaranteed to be correct. In fact, I should mention that I am a software guy and my hardware skills are a sideline, so you might take my interpretation of the circuitry with a grain of salt. If you spot mistakes or if you just happen to understand this stuff better than me, please let me know and I can fix these diagrams.
So if that is enough disclaimers, the schematics can be found below as '.png' graphics files. Each sheet is commented with my understanding of how the circuitry works.