Quick fix for the rust is to spray WD-40, or as I prefer, LPS-3 which is like WD-40 but does not evaporate as quickly. Thats to slow down the rust significantly. Many places where you pictured like under the car, you can get rid of it by just sanding it down.

For the headliner, the drain tube which drains water which enters through the gaps in your sunroof is disconnected. You can easily take apart the rear trim and headliner to re-attach the hoses. Make sure they are not plugged.