I have heard that there is a small number of textual differences between Teimani torah scrolls and Ashkenazi/Sefardi ones. What are these differences? If I encounter a manuscript of unknown origin and want to know if it's Teimani or Ashkenazi/Sefardi, where are the places I should check?
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The nine places where a different letter (style and layout differences aside) appears in modern scrolls are:
However, I would not recommend using these as shibboleths for locating the origin of an old (<1700) manuscript. Before communication and printing became so widespread, things weren't always so uniform and variations like these were a fact of life. As an example, the influential Ben Hayyim edition of the Mikraot Gedolot (1524) has #1,2,3,5,8,9 from above written the "Temoni" way. Granted that edition wasn't without its share of typos, but it was being printed in Venice, far away from Yemen, and probably was reflective of some local practices.
To bring the point home, R Moshe Isserles, perhaps the epitome of an Ashkenazi rabbi, himself wrote a Torah scroll from a rare and expensive manuscript. (The story goes he bought it from R Yosef Karo from Safed.) The scroll and manuscript were kept securely in Crackow and highly venerated, before apparently being burned by the Nazis during the Holocaust. In the journal HaMaggid on April 28, 1858, someone reports that the Rama's Torah had 14 letter-differences from the other Torah scrolls commonly used there (* indicates the variant is also found in the 1524 Mikraot Gedolot): *Gen 4:13 מנשא; *Gen 7:11 מעינת; *Gen 9:29 ויהיו; *Gen 36:15 תומן; *Gen 39:22 האסורם; *Gen 41:14 וירצהו; *Gen 46:6 מקנהם; *Exo 10:9 ובזקננו; *Exo 28:26 האפד; *Exo 29:15 אהרון; Num 1:17 בשמת; Deu 13:12 וייראון; *Deu 23:2 דכא; *Deu 32:34 הלוא. None of those variants are in modern "Ashkenazi" scrolls. (There might be reasons to think that parts of that list are inaccurate, but it seems clear the Rama's Torah scroll wasn't the same as ours.)
The relative uniformity of our scrolls today (as well as the notion that there is such a thing as an "Ashkenazi" tradition or a "Sefardi" tradition; it used to be a scribe would just seek out the best most reliable texts available to copy from, as the Rama did) is a relatively modern phenomenon, growing largely out of widespread distribution of mass printings and the work of certain rabbis to fix errors in them (to oversimplify just a bit). When the Rama (!) rules (OC 143:4) that we don't put back a Torah scroll for having extra/missing matres lectionis because who says one scroll is better than the other, he wasn't just stating a hypothetical.