From the same site:

Train timetable of G2 from Shanghai Hongqiao to Beijing South. All data are the newest and last updated: Jan 1, 2012.
Station Arr. Dep. Dist.(km)
1 Shanghai Hongqiao - 09:00 0
2 Nanjing South 10:07 10:09 295

That is definately high speed.

Due to some flight cancellations, it looks like my best option out of Nanjing is actually a 1:45pm flight from PVG. I'm guessing that if I try to leave around 8:00 I should be able to make it there. (Though, I should probably aim for earlier to handle getting lost...)

I see trains going to two different stations in Shanghai. Is one of these stations preferred to the other?

Not really, just depends on your location and ease of getting to either Hongqiao (by the airport) or main station (in Zhabei).

Looking at the schedule, it seems that G7495 would be your best bet:

G7495 高速动车 蚌埠南 南京南 09:39 上海虹桥 买票 转让 求购 上海虹桥
10:59 上海虹桥 1小时20分钟

Fox: in the OP's case, Hongqiao is categorically better than Shanghai Stn, because: 1) the fastest trains terminate there; 2) almost no traffic between there and PVG; and 3) the #1 bus is nonstop... as opposed to the #5 bus from SH Stn.

That having been said, this is one of the few scenarios in which I would actually advise a PEK connection.

Just did Nanjing South - Shanghai Honqgiao on the G51 (interesting Tianjin - Hangzhou routing) yesterday in first class. It's really amazing how quick and comfortable the journey is compared to years past. We had one stop at Suzhou North on the way, total travel time was around 1h15min.

On the other hand, I was coming from the southern outskirts of greater Nanjing so 南京南 was easy to reach. Also well connected to the airport well south of the city centre. However, it's really not that convenient from downtown Nanjing.

Btw, for fast food aficionados, 南京南 has an Carl's Jr. outlet on the departures floor.

As for transport from Honqgiao, I'd still advice people looking to catch a cab head over to SHA T2 or even take line 10 two stops to SHA T1 like I did yesterday. No waiting at all at the T1 taxi stand. The lines at the railway station can be enormous, especially during the Spring Festival rush lasting well into February.

Assuming he can't swing a better itinerary, our OP should take the #1 bus to PVG, plain and simple.

But, for local traffic, I'm now convinced that the subway (line 2 or 10) is absolutely the best way to/from SHA (T2 is a surprisingly long taxi ride from town).

And buying tickets?
 

Is it easy to buy same day tickets at the train station. (For Shanghai-Nanjing and Nanjing-Shanghai). Or should I try to get one in advance? (Can you buy tickets in advance outside of China?)

HS train you should be ok at the station.

Since he needs to get a ticket on a specific train or two, he should buy in advance IMO, on the official website or at his hotel.

If he can swing it I'd say yes. But my guess is 99% of folks couldn't navigate the railway site (mostly due to Chinese).

Just buy the ticket at a major hotel - there are plenty of them in Nanjing.

The train station is easily accessible, and if you are worried about traffic the metro doesn't take that long to get there either.

You want to get to PVG? Lots of options available. Bus, taxi, subway....all of which will get you there easily before a 1:45 departure. Go for the #1 bus.

It turned out to be pretty easy. After I arrived, I took the maglev (I had too...) to the #2. Took the subway to Nanjing road. Walked the road (and must have had a sucker tag attached for all the 'offfers' I received.) I walked to the next station and continued on to Hongqiou.
There I tried to buy a ticket for a train that I thought left in 15 minutes. The guy told me that I couldn't (I really need to work on my Chinese) and I got a ticket for a train that left in an hour or so. It made just about every stop, though the first class compartment was pretty empty.

I got to Nanjing station, and easily made it on the subway to my hotel.

For the return, I had the ticket purchased in advance.

I went from Nanjing to Shanghai main station. There was one stop and it took about 90 minutes. From there it was another 90 minutes to the airport. (But that included a lot of wandering around aimlessly at the train station and a visit to the Maglev museum.) I was at the airport ridiculously early.

Alas, hasn't quite caught on with the locals yet. The place is usually deserted, at least compared to the ones in Shanghai