Here is my take on the report:
Negative grading can be corrected by the use of soil and power equipment, such as a Bobcat. A landscaping company could come in and re-sculpt the terrain, so that water can be directed to where you wish it.
To answer this, the sheetrock would have to be opened so that a more through inspection could be made. It might involve drilling a small hole so that a small inspection camera could be put behind the drywall, or perhaps an opening big enough to stick your head into could be cut. Then you would know if it is a serious problem, or something as easy as sealing a window on the floor above.
Leaks at the p-trap can usually be stopped by tightening the fittings. They can loosen up over time, especially if the vanity in not screwed to the wall. I need a photo for the stopper arm.
The flue can be secured with a couple of sheet metal screws. The transition fitting can be purchased at your local big box store. It is easy to install.
The sleeve is merely a piece of plastic that the pipe would run through. The builder forgot it. Someone would have to disconnect the pipe, make sure that the hole in the brick was large enough for the plastic to go through, slide a sleeve over the gas line, and seal everything up. Oh, and re-connect the gas line. It's a $1 piece of plastic, but might take an hour to install if the have to drill a larger hole.
Mold can be caused by condensation in an attic. Someone should go up there and check to see if, for example, a bathroom vent is discharging into the area. Ventilation should also be looked at. Soffet vents, a ridge vent, maybe an attic fan to help with air exchange. If moisture get into the attic, it needs a way to get out.