Unfortunately, I'm not qualified to really help your exact question. However, it should be noted that the Russian Civil War displaced and killed a lot of people, and the Russian Empire had problems with pogroms against Jews. It's not inconceivable that many of those towns were depopulated as a direct consequence of not just the Russian Civil War, but also the actions of the USSR before WW2.
My first thought at the mentioning of the underrepresentaion of Jews in gulags was questioning how many had simply been killed outright instead of imprisoned, or simply fled the town/country before then. I'd look into the numbers of Jewish people who fled the USSR after 1900 to get a clearer picture.
Overall, the history seems pretty accurate to my knowledge, but again, I'm not an expert by any means!