Use a slower shutter speed next time will help reduce the flickering and scanning. You might be able to get away using a little compositing. Capture a screenshot by hitting the "Prt Sc" button usually up there by F12. Open up MS paint and paste the picture where you can then save it as a jpeg or bmp. Then import the image into your footage and resize to look like it is fitting in monitor frame. Next, you'll need a mouse icon that you can animate moving around and clicking on things.
There is also a freeware program called Wink, which does something like this but the output is to flash,html, PDF, or an EXE... but it's worth a look
http://www.debugmode.com/wink/