Hi
the Tenere airbox has three connectors for that crankcase breather size, one on the left hand side and two on the right hand side.
There is a short vent on opposite sides, and the leftover connector is for that 12mm hose as explained before.
I only found a picture where part of it is shown, left side, click for bigger pic:
For the fuel pump: most people I know get rid of it. Just connect fuel taps to the carb inlet and plug that vacuum connection of the left intake and you are good. The fuel pump can caus all kind of troubles, especially when switching to reserve it can draw air and render the rest of the fuel useless - it will not get to the carb any more when there is an airlock. You only loose about 0,5 litre of fuel by getting rid of the pump.
If you still have questions it would be extremely helpful to post some pictures of the problem area. Maybe you have modified parts or parts from a different model on that bike.
Andy