Dear Chaim,

The Maharal says that even though we are not sure if our Sefer Torah has all of the correct letters, we may use the Sefer Torah as is, unless we know for sure that a letter or word is missing (in which case it is Pasul for sure).

He then answers that for the Mitzvah to write a Sefer Torah, it must have every letter, but in order to read it for Keri'as ha'Torah (on Shabbos, etc.), we fulfill are obligation even with parts missing (without elaboration on the maximum permitted), and it even has Kedushas Sefer Torah.

He quotes several Halachos of Megilas Esther (how much can be skipped at the beginning, reading words by heart that are not written down), and discusses what this implies in the case of a Sefer Torah, discussing whether it is more or less severe than a Megilah. He remains with what he explained earlier, that for Keri'as ha'Torah, even when parts are missing it is Kosher.

All the best,

Reuven Weiner