I first heard about large-scale Xinjiang conflict during the Sion-Vietnamese war. Col. Harlen Jencks, the PLA expert at Cal, corrected me when I said the PLA hadn't seen real fighting since Korea. His example was Xinjiang.
Naturally, written sources are few and far between for such an embarrassing and enduring internal conflict. From my own library, I found these references:
From China: The politics of Revolutionary Reintegration, by James Seymour, 1976, p. 236: Reference to “major uprisings” in the late 1950s and early 1960s.
1961 Yili Valley revolt. 1963 USSR accused of fomenting Northwest Xinjiang unrest, (1967 Area Handbook for Communist China, p. 424-425)
1959. “In Hentin, some 10,000 youths were said to have attacked a local prison, freeing some 600 inmates, killing 50 prison officials and seizing stocks of grain.Depots were burned and communications facilities were harassed. According to one source, large military reinforcements were required to put down the uprising, which presumably lasted for nearly two months.” He also mentions very bloody clashes in 1967 known as the Shihezi Incident that involved “ten truckloads of armed troops.” Scores killed. Summer 1969 Soviet incursion into Tacheng, Yumin and Khabaho, including tanks. (Chinese Communist Power and Policy in Xinjiang, 1949-1977, by Donald H. McMillen, 1979.)
“An unreleased study by the Rand Corporation listed three thousand instances of civil violence in the year 2000 alone.” and “Even though the few large-scale incidents in the 1990s were better publicized than those of the 1980s, they were not necessarily bigger or more threatening to the state.” China's Internal and External Relations and Lessons for Korea and Asia, Jung-Ho Bae and Jae H. Ku, eds., 2013, p. 61-62)