yes, the chinese version of ctrip also has the schedules available.
for work i go back and forth between Shanghai-Nanjing a few times a month (1 hour 59 minutes the fastest i've done so far - T31). First class is comfortable (~100 RMB one way), and definitely worth the little extra over the standard seats.

I only take the car if really necessary, the train shaves about an hour off the travel time. Both train stations are pretty much downtown in both cities. Though i never catch a cab, i usually see pretty long lines at Nanjing, so this may be tricky (especially when its raining).