TTY so I can print off
I have never done a project that large before but have made smaller ones also. I usually mark my graph with colored pencils and end at the end of a row. On one that size It might work if you string an extra needle with single strand of DMC floss and every so many beads run your needle through the bead and snip it leaving it hang out like a short beginning thread. That way you can count your threads by tens or twenties and at the end of a row just slip them out. It might be a little more time added but for piece of mind and ease of counting it might work.
I have been reading this thread, and wanted to give a tip on how to keep your place on a chart.
In the cross stitch section of your local craft store, they have metal sheets with magnetic strips. (Or you can just buy magnet strips, and use a cookie sheet.) The metal sheet (cookie sheet) is a great flat surface. Put your chart on top of the flat surface, and use the magnet strips to both hold the chart still, and mark your place.
If you make a copy, you can also make a mark at the edge of the chart with a pencil.
I don't recommend using a highlighter or a pen on your charts, as sometimes the ink won't dry quick enough to keep it from getting on your hands. (I'm left handed, and normally end up with ink on the edge of my hand, which can end up on my craft projects.)