Handling this data in a spreadsheet is terrible: it's unresponsive and consumes loads of RAM. This made my computer unresponsive for a few hours! Remind me never to do this again....
Have you ever tried Gnuplot? From own experience, it handles large datasets to produce a graph quite nicely. I didn't look at the original data and therefore can't say what amount of "data massage" is needed to get the correct data to plot.