I think a lot of what you're seeing has more to do with the "soup of story" and the writer's craft than symbolism per se. I've read an article that shows quite clearly instances of the influence of World War One on Tolkien's description.
- The Dead Marshes with the dead faces in the water, straight out of the Western front.
- Tolkien said, "My Sam Gamgee[...]is a reflexion of the English soldier, of the privates and batmen I knew in the 1914 war, and recognized as so far superior to myself."
(By the way, that more or less explodes the idea of Lieutenant Tolkien as a leader of men - he spent the bulk of the war in hospital recovering and relapsing with the fever.)
-The final Shadowy aspect of Sauron defeated, as a threatening cloud, has been compared to Sigfried Sassoon's description of a shell-burst at close range.
- The Hobbits' return to the Shire mirrors the war veterans' return to an England that had during their absence changed from a semi-medieval rural society to an modern industrial one.
As to the party turned problem angle, that's just the nature of good writing, perhaps especially fantasy but not exclusively. Things start out idealically, and the conflict is introduced. Otherwise you don't have a story.
As to your sequence of three's, I think there might be something to it, although we are supposed to be in the seventh age, right now. But I don't think there's as much to it as you might hope. Nevertheless, numbers were important to Norse and Celtic pagans, and since Tolkien dipped his ladle in those vats, it's no surprise that he came out with significance in numbers. More significant is his lingual treasure.
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