I noticed above that deepbluehum posted that the number counting (in ngondro, I'm guessing) started in the 13th C. I'm curious about the history of this number counting and I wasn't sure that people were doing ngondro in the 13 C. so if there are any leads about this I would appreciate hearing about it.
So if deepbluehum or anyone else knows about these topics please let me know.
People did Ngondro, but the overall systematization of Ngondro seems to be a rather nineteenth century phenomena that spread from Kagyu to the other two schools i.e. Nyingma and Sakya. For example, the massive 350 folio commentary on the Lam 'bras preliminaries authored by Zimog Tulku in the nineteenth century was explicitly influenced by Kun bzang bla ma'i zhal lung. Before this text, there was no separate Sakya Ngondro commentary. And the first independent Ngondro text in Sakya was written by Dezhung Rinpoche.
However, there was ngondro from an ancient period of time. For example, the klong gsal nyi ma 'bar ma rgyud [which probably dates to the 13th century and is the root tantra for the mkha' 'gro snying thig] has a fully elaborated ngondro from chapters 63-75. For example, the refuge chapter, 67, does not give a number. Chapter 73 specifies doing Vajrasattva for 21 days, for example.
In general, I think the idea of doing 100,000 thousand comes from the idea of reciting mantras 100,000 times in the gsar ma tantras.