The story that Pashtuns have a Jewish connection is not factual. The "lost tribe" aspect was most likely promulgated by 19th century British explorers and missionaries. I lived for two years in the 1960's in Kandahar, the Pashtun heartland, and I have remained in touch with many Afghans ever since. I have never met a Pashtun who referred to the "Bani Israel" in reference to their genealogical history.
In reference to the AJEX Newsletter article:
1. Pashtuns don't have a tradition of "lighting candles on Friday night". If they do light candles it's because they don't have electricity and they light candles/lanterns every night and not just Fridays.
2. Pashtuns don't separate milk from meat. In fact there are popular Afghan dishes in which meat is served with yogurt based dressings.
3. The deceased are generally wrapped in a shroud when buried (no coffin). After being placed in the grave a decedent may then be covered by a stone or board and then covered by earth. At the burial a stone is generally placed on the ground over the area of the head and of the foot of the buried person. I don't know of any tradition of placing stones on graves as a sign of a visit as is often done in the Ashkenazi tradition.
There were two small communities of Afghan Jews in Afghanistan when I lived there; in Kabul and in Herat. All but one of the Afghan Jews have emigrated, most of them having gone to Israel and New York. Currently the only Afghan Jew remaining in Afghanistan lives in Kabul.