Hmmm, haven't been to the Stout mines for a while, but let's see if I can help.
The trolleys have two starting points, but the right hand one has two junctions. Leading to a total of four destinations. Have you explored all four? One of them leads to an abandoned trolley line. Walk down it and you will find the lava lakes. The ore is here, you just have to deal with a few cute lil'old lava puppies first.
The tedious part is all the running back and forth to keep switching those d@mn junctions.
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