Re: Air Filter Question and brake noise.
I'm assuming you're talking about the 2 spouts that come out the top of the airbox as shown in my pictures. They actually join onto the exhaust manifold just after it exists the head. I believe that it is emissions related and recirculates the air from the exhaust back into the intake. They were probably disconnected in the hope of gaining a little bit more power.
Clean air should be entering from under the filter, traveling up through the filter, then outwards into the carbs. The silver tube going to the front of the car in my second picture (top of pic) is bringing in the fresh air. This connects down at the base of the airbox on the passenger side. There should be an opening there for it on your car too.
As for the brake problem, I'm not too sure on that one. My only suggestion would be bleed the system thoroughly and put in new fluid.
The rear light problem would most likely be caused by some corrosion on ground wires, meaning that they're not making proper contact.