First, I echo what Paulchen says about John and his visions recorded in Revelation—those have nothing to do with canon. I also echo his thoughts about being submitted to Scripture in the sense that we can’t include or exclude books from the canon simply because they rub us the wrong way. However, though our preferences shouldn’t guide how we think of the biblical material, our critical minds should. “If you start questioning which bits of Scripture are more true than others, you start judging the Bible.”

I’m not sure about your use of the word ‘judging’ here, but if you mean ‘thinking critically about’, then I would argue that’s a good thing. There is a an important difference between treating biblical writings frivolously (which is, I think, what you’re afraid we might do if we disregard the canon), and treating them well by thinking critically about their content. What I’m saying is that there might be cases in which a disciple of Christ is called to wonder about, and investigate, which of two parts of Scripture is ‘truer’ than the other.

Am I making sense?