It has taken me five months to read this. I found I could not proceed faster than one canto every day, and on many days I did not manage any cantos at all; and there are 74 of them, plus the proems and the two concluding verses. It's not that it is particularly difficult to read, compared even to Shakespeare; the style is generally consistent, and a good edition (mine is the Longman edited by A.C. Hamilton) helps you through the more obscure words or usages. But it's dense and moves both rather slowly and rather fast at the same time.
I found that one of the biggest barriers to my understanding of the poem was Tolkien. Spenser writes of elves and dwarves in a parallel fantasy world, but these are not Tolkien's separate races; the elves are effectively just a fantasy nationality, and the dwarves just short guys (who tend to appear as servants). I was also subliminally expecting some Big Bad villain, but in fact we have a chain of more or less loosely connected stories, with the main linking character Prince Arthur, who is intended to be King Arthur (and yet didn't fit for me too well into my own vision of Arthurian legend). So I found myself unnecessarily distracted by my attempts to fit it into fantasy genres with which I am more familiar.
What does come over with extraordinary vigour is Spenser's love of the Irish landscape. Subsequent history shows him as one of the many adventurers who descended on Munster to occupy land confiscated from the Desmonds and their affiliates, who then lost it all in a subsequent rebellion; it's worth being reminded that from Spenser's point of view, he had come to stay, and expected his descendants to live on at Kilcolman for many generations. County Cork was his home and the focus of his imagination. It's not too difficult to believe that he died essentially of a broken heart after losing it all.
As for the actual meaning of it all: I think it is possible to over-analyze. Sometimes the allusions are pretty obvious, or indeed the description may be pretty much what it appears to be (thinking for instance of the house whose chambers correspond to organs of the human body, or the personified rivers of Britain and Ireland). The only one of the six virtues where Spenser has much interesting to show about the virtue itself, for my money, was Courtesy; I felt he let his pen wander aside from the point as his fancy took him elsewhere. The best character in it is Britomart, who is obviously the model for George R.R. Martin's Brienne of Tarth.
And there's a robot, but that needs a separate post.