Thanks everyone for the advices. Now I have got my deposit back. Here are the details:
When the first day I went to check the work of the painting and floor, I pointed out the paint showed differently than the old one. The contractors said it’s because of difference of new and old paint. Maybe even the contractors themselves were not happy with that result, or maybe they found it took them much less time than they originally estimated, so they decided to do a better job. Anyways, since I just bought a house, I could be their returning customer for bigger projects. The next day when I came back, they surprised me with a very nice job. They painted the walls where they looked ugly from top to bottom. They also refinished the floor where it was scratched. The whole house looked even newer than the time I moved in! I was very happy.
I called the landlord in for the final walk. She was very happy to see the house was in such a good move-in-ready condition. But she still pointed out the door from the garage to the kitchen was dirty, which was overlooked by both my contractors and me. She said she would try to scrub, but if the dirt stays, she would charge me the price of a tin of paint. She also asked me to remove any garbage/boxes left at the house (out of the garbage cans), otherwise she would charge me disposal fee. Other than that she would return the rest of my deposit in 21 days.
In 3 weeks, I received my full deposit back. Not sure if my landlord managed to clean the dirty door, or she just let it go.
Over all, I spent $600 on contractors, $180 for cleaning, and $220 for days of rent when the house was empty, which add up to $1000. Still expensive, but much less than the total of the first round of quotes. I think the contractors for painting and flooring overcharged a little, as these two people charged me for two days work, while in fact it seems they could finish in one day. But they did do a good job in the end of the day. I did hire them back to help on my newly purchased home. I heard many anecdotes in Bay Area about some contractors disappeared in the middle of a project. In comparison to that, these two guys are not bad.
I know many people can manage to minimize the move out expense better than me. I am ok with that. I am satisfied that I could leave the headaches of past behind and focus on what I care and would like to spend my time and energy on: organizing for my future home, while work full time and take care of my two children.