The sensor between the MAF and air box is the air temp sensor (often built into the later MAF's).

The stub is basicaly a matching device used on transmission lines (or on this case an air system but, similar principles), it will flatten out the torque curve by absorbing air pulses from the engine.....

The Bosch leads are good, they dont seal very well with the cam cover but, that shouldn't cause to many problems as there is a cover over the top of them.