Sounds like you've done your research and know what you want to do!
Some suggestions:
Don't rent a car until you are ready to leave SF. Hotel parking starts at $30 per day and if you are going to use MUNI to get around you won't need the car. Even taking cabs to/from your destinations will be cheaper than the car rental/parking fees.
Skip the 2 hour cable car tour. It is basically a tacky bus that is open to the elements. If you must do a riding tour try one of the smaller, quirkier tours like the Ducks, Mr. Toads, or the Segway tours. SF is very compact and you can get around quite well. If you don't have mobility issues you may want to consider a walking tour. It will give you some info on history and culture and your guide can give you helpful info regarding other areas of the city you might want to explore.
http://www.foottours.com
Limit your time at the Wharves to the time it takes you to get to and from your bay cruise. The area is basically an overpriced tourist trap with bad food, and lots of junk. The cruise is a great way to get out on the bay and see amazing city views. You can do the chowder bread bowl thing here or at Union Square, Bodin has locations in both areas.
Specifics on your list:
union square- mostly want to visit tiffany's and miette bakery.
You can do US very quickly if you are limiting yourself to only a few stores. There is not much else to do there but shop. So this could be done the day of your bay cruise or walking tour.
Combine these two
haight/ashbury area & vintage shopping there
golden gate park (possibly the conservatory of flowers)
GGP is huge and there is a lot more to see than just the conservatory. Don't miss the Arboretum and Japanese Tea Garden. There is also the Deyoung Museum and the Academy of Science. Limiting yourself to only 3 of the above is going to take most of the day. You'll be in a good position to do the Haight before or after the park
Combine these three in one day.
walk on golden gate bridge - plan an hour and half if you want to walk the entire way. Walking half way and back will take about an hour. From the SF end of the bridge go down and explore Ft. Point [surfers, seals and unique views of the bridge]. Then make your way to Chrissy Field.
End the day by checking out the fillmore - mostly shopping. Japantown is worth a look and if you want Jazz, check out Yoshi's, Rassallas, and 1300. For blues visit the Boom Boom Room.
These two are in North beach and would take most of one day.
Cafe trieste for breakfast then explore North Beach a little. Be sure to stop by City Lights and the Beat Museum. Lots of cool little shops and great food. Near Trieste is one of the City's best Italian Delis Molinarie's on Columbus at Vallejo. Get sandwiches or salads and drinks to go and take them with you to Coit tower. After you have seen coit tower take the Fillbert Street steps down to the Embarcadero. Incredible views of the Bay and a visit to one of the most unique neighborhoods in the city.
Other areas you may want to check out. The Mission-from 15 to 24 along Mission and Valencia lots of incredible thrift/vintage stores, boutiques, and restaurants.
Chinatown - the largest Chinese Community outside of China. The best place to purchase souvenirs to take home to friends and family as well as authentic Chinese food.