The Tenderloin area should be avoided at all costs. Do not stay there! Fishermans Wharf is a little bit of a tourist trap. It's best not to plan a whole day around it. Check out the area guide under the travel tab for general recommendations on where to stay
If you are used to city driving and dont mind circling the block to find a parking spot then a rental car may be the most efficient means of getting around the city. You can knock out a lot of sightseeing this way (ex. driving down Lombard street or across the Golden Gate Bridge). GIG car share is a great way to rent a car for a day or even just a few hours: https://gigcarshare.com/bay-area/
Yes- If you would like to visit Alcatraz Island or Muir woods, you will want to book these at least a couple months out. Airbnb's and Hotels should also be booked in advance.
September is one of the warmest months in San Francisco but you should still prepare for chilly and/or windy evenings. Do bring- Light jackets, comfortable shoes, sunglasses, camera Dont bring- Shorts, sandals