I often do something similar. Fly into Pudong then I take the rain in Hongqiao to Nanjing.
I usually book a train at a comfortable time and if I arrive early in Hongqiao then I go to the counter and exchange for an earlier train. This way I am sure of having something.
Last time it was fairly quick. I was out of the airport in 45 minutes. I jumped on the Maglev then switched to the subway. All in less than 2 hours. Travel time via Maglev-subway is quite predictable. Getting through immigration can take an additional 15 minutes if things are bad. The wild card is time of arrival of your flight.