While I was in rush hour bumper to bumper traffic I decided to try it out using the manumatic. So my questions are:

1) At what rpm should I shift up?2) What is the top speed for each gear?

I was shifting up when I was getting close to 3000 rpm's and was in 5th as low as 40 mph. Is this correct?

There isn't one set speed or rpm that you need to shift at, it depends on what you are trying to do. If you are strictly trying to get good fuel efficiency then shift early, like maybe 2000 rpms. If you are trying to get performance and maximize the power output and acceleration of the vehicle, you can shift at 5000 rpms. There really isn't a top speed for any gear, the top rpm would be the red line. If you are concerned about the engine and tranny working at optimum efficiency, let it shift automatically, and when you want to have fun, use the paddle shifters. Also, if you are really shifting incorrectly, such as trying to upshift to 5th gear when you're only going 20 km/hr, or trying to drive 100 km/hr in first gear the transmission will override your gear selection to protect the mechanical components and select a more appropriate gear ratio for you, so you don't have to worry about damaging anything.