from Pudong airport to Nanjing street, which subway line should I take?

1. Upon landing, you can take subway line 2 at the airport, and get off at East Nanjing Road Station, Exit 2.
2. You can suggested to go to Nanjing Road first. After that, take subway line 2 at People's Square and go to Lujiazui Station, Exit 1. Then walk northwest around 400 yards to find the scenic spot.

how long taking from Pudong airport to Nanjing street, and from Nanjing street to the tower? And if I take taxi direct from the airport to Nanjing street, how much it cost and how long it take?

1. The distance between the airport and Nanjing Road is about 30 miles. The cab fare is CNY 180 to 190 in the day time.The duration is 30 to 40 mins.
2. The distance between Nanjing Road to the Tower is about 4 miles. The cab fare is CNY 20 to 30 in the day time. It takes around 15 to 25 mins on the way.

Is subway line 2 available anytime or it have time schedule to travel between both places? which line should i take from the tower to Shanghai South station, how long it take and how much it cost? If travel with taxi to the station, how much it cost?

Well, the operating hours of subway line 2 are from 6:00 to 22:00.
Do you refer to South Railway Station?
If yes, you can take subway line 2 at Lujiazui Station, get off at People's Square Station. Then transfer to line 1 to arrive at South Railway Station. It takes around half an hour on the way. The tikcet fare is CNY 4 per person.
If by taxi, the fare is CNY 60 to 70 in the day time.