When I was gunning E-Hill at moab some years back, a guy had the retaining pin in his cross shaft break, allowing the cross shaft (pinion shaft in Toyota vernacular) come loose in his front ARB'd diff, effectively "locking" his front axles from turning. The cross shaft then opened up a nice air conditioning vent in the front of his diff housing. Fortunately this was at the start of the trail, he and his wife parked and rode with others.
Just sharing a failure mode I have seen first hand. No idea if it's the related to your issue. I have pulled several cruiser 3rds which had a broken, but still functioning cross shaft retaining pin. I know that mini/runner 3rds use a drive pin for this and cruisers use a threaded fastener, but it still might be something to look into.
I know it's major PITA, but pulling the 3rd and doing a visual inspection would seem in order. If you have a spare 3rd, maybe swapping it in to get around to the ARB might be a little less work...nah. But like you wrote, having it grenade would be worse.