1) Don't change the wheels because the heavier rim will eat through your control arm bushings. The car already has 235 width tires, you have an S320, I dont think the car needs the extra tread. Save your money for the head gasket repair.
2) The glass is double pane and I know some pieces are very expensive.
3) Almost anyone can install the navigation systems these days; but I would have it done at the dealer or a reputable shop for a nice clean installation.
4) Rear AC. I bet it could be done but the cost would be very high. The cost would be at least 2000 since it was a 1500 option from the factory.