You didn't say which bike you have (1G or 2G, 600 or 1200), so I'm just going by what my bike has (a 2G B12). The connections in that area on mine are normal wiring loom connections. The ignition control box lives in the tail and wires coming up from the motor are for neutral and sidestand safety, alternator, and ignition signal. The stater relay is also in that area.
On bikes that have any retard feature (and US bikes don't), they take a signal from the gearbox switch to retard timing in certain gears (2nd & 3rd, IIRC).