photo 1. that tube feeds air from the intercooler pipe right before the throttle body, into the idle air control valve (iacv). if you are not using the iacv feel free to cap that whole thing off or make blockoff plates, etc.
photo 2. that tube normally runs to the oem oil catch can, personally i run a hose straight from the valve cover fitting right above it, into the metal tube in your photo.
photo 3. yes its the coolant line for the turbo. i happen to have a stainless line for sale for this made by DIF. its the coolant line from this kit, but i only have the coolant line, not the oil lines available
DIF 10034 Bottom Mount Turbo Coolant & Oil Lines Kit S13 SR20DET (OE)
pm me if interested.