I will focus on the two parts of the question that have not been addressed yet: "What accounts/sources exist about these skirmishes? [...] What were the outcomes of the skirmishes?"
the most substantial account I've found so far is a single paragraph in this article, "The Form of a North Borneo Nativistic Behavior":
On December 17, 1941 the Japanese invaded North Borneo with a force of 25,000 men. Main centers of occupation were established in the Murut area at Tenom, Keningau and Pensiangan. For three years, large patrols of infantry regularly moved from these points through Murut territory, conscripting labor for construction of military airfields, women for army prostitution centers, commandeering rice and other foodstuffs, imposing head taxes, fines and punishing offenders. In late 1943 allied guerrilla agents, parachuting into the area, enlisted Muruts in a force for raids on Japanese patrols and outposts. Re-occupation of North Borneo by the Australian Ninth Division led to heavy fighting through Tenom and Keningau. The 6,000 Japanese stationed in Pensiangan were ordered to stack arms and march 150 miles to the coast at Beaufort. Australian army records show some 400 Japanese reached Beaufort. The remainder were killed by Muruts along the line of march (Tregonning 1958: 221).
Wikipedia has briefer mentions of indigenous involvement in the Jesselton uprising and operations like Agas and Semut. None of this refers directly to blowguns or other traditional weapons.
EDIT: I will try to watch the video and expand this if I can. The description on YouTube refers to Dayaks of which the Murut are one of many subgroups.