For your exhaust vents: It looks like right now you've got that big OPEN vent across the top. There are also some solids that have been canceled out by some holes. Were these solid chucks previously the obstructions to which you attached your exhaust vents? If that's the case, the most common cause of your problem is that the place where the vent was supposed to meet the obstruction did not lie along a grid cell boundary and the vent resolved to a different place than the obstruction (causing them to not be pressed together in the simulator).
I'm hoping questions 2 and 3 fix themselves when you get your vent issues resolved.
To make any vent or obstruction invisible in Smokeview: right-click the object in the tree, then click Hide Object(s).
The chunks in the air were the holes i made in the roof ostruction above the vents, i'll give it another go, thanks for your help.
Its running better now that the floor is gone