You’re asking good questions, but I don’t think you’re taking them far enough.
How reliable can these stories be if they weren’t written until 40–60 years after the crucifixion?
I think the more pressing question is, how reliable can these stories be if they don’t agree with each other on key points? If Jesus was indeed born of a virgin (which was not prophesied in the Old Testament and was only considered an omen due to a mistranslation in the Septuagint), why do not all four gospels reference such a remarkable occurrence? Why do they not agree on his place of birth or genealogy? Why are events of remarkable import mentioned in some gospels but not others? This makes the reliability of the gospels dubious even aside from their date of authorship, but this does not mean that we cannot gain any knowledge at all concerning the historical Jesus. We can evaluate the accounts according to three criteria. If something occurs in several different, independent accounts; and if something is expressed contrary to the vested interests of the authors; and if the event or saying in question makes sense in the context of 1st century Palestinian Judaism, then it is very likely to be historically accurate. But very little of what is contained in the gospels meets these criteria.
More pressing as well is the issue of there being over 5000 extant copies of Greek documents from the New Testament, no two of which are alike, the earliest of which (and these are only fragments) having appeared in the 2nd century CE. It was not until the 4th century CE that we have complete manuscripts. These manuscripts predate the printing press by centuries; they were copied by hand from copies made by hand from copies made by hand from copies… so on and so forth across over 300 years, with mistakes and deliberate alterations creeping in the entire time.
You are correct that historians presuppose no supernatural intervention in the authorship of the Bible. This is entirely necessary. What justification would we have for presupposing actual occurrences of prophecy? Only the Bible itself, and to take that as sufficient is circular. If the Bible were historically reliable in general, then its claims of prophecy might carry more weight. But we cannot say that seeming anachronisms are due to prophecy based on the justification that the Bible is prophetic because it contains anachronisms.
Your counterpoint to this is that the authors could have been more detailed in their description of prophecy, but that would presuppose that the authors had as much information about the events that had transpired as we do, or as Josephus had. In an era when books had to be copied by hand, would even educated gentiles have read the works of a Jewish author from a distant city only a few scant years after their publication? The Jewish War was only even completed in 78 CE. What the authors would have known of events such as the destruction of the temple would have been primarily from word of mouth.
But let us assume the authors did indeed have an accurate account of the destruction of the temple. The ancient world was rife with forged documents, some of which even made their way into the New Testament. Often these documents were written so as to appear as though they had been written in a prior era. Both authors and readers would be looking at documents and asking the same questions that you are, and authors would know that these questions would be asked of anything they wrote. Had a more detailed account of the destruction of the temple been available to the authors of the gospels, they may have wanted to remain vague regardless to avoid the appearance of forgery. In a world where scholars must constantly be on the lookout for forgeries, an especially detailed prophecy might have been seen as too on-the-nose to be believable.
One might also point the question in the other direction: if Jesus was able to prophesy the destruction of the temple, why would he not have been more detailed? Why would he not give any context or a more specific timeline? Why was this prophecy fulfilled but not others that he made (such as Matthew 16:28)? Surprisingly, you haven’t mentioned that even the agreed historical dating of Mark is only just after, or even shortly before, the destruction of the temple. Given, this, Mark 13 is indeed remarkable. This foretelling is also something that occurs in all three synoptic gospels and that was consistent with the overall apocalyptic message that Jesus was preaching. With regards to the author called Mark, the prophecy of the destruction of the temple seems to stand in opposition to his vested interests: no one would have expected that the Jewish temple would have been destroyed after the coming of the Jewish messiah.
So, it does indeed seem to be the case that Jesus foretold the destruction of the temple, though in the vaguest possible terms and clearly in the context of Jesus’ apocalyptic message that all things, temple included, would be destroyed in the final judgement. And since that judgement never occurred, and certainly not within the timeline he gave, Jesus’ prediction cannot be considered prophecy.
Here’s another question: if the gospels were authored prior to the Pauline epistles, why does Paul not reference them? Why would he not directly address conflicts between his teachings and what is said in the gospels, given that he so thoroughly addressed each new conflict that the new Christian communities had come across? You mentioned 1 Timothy 5:17–18 and also mentioned the dubious authorship of that book (which I’ll address presently), but gave the dating incorrectly. The dating of 1 Timothy as between 55–64 AD is based on the assumption that they are authentic, but there are more reasons than just the quoting of scripture to believe otherwise. The main one is that the text seems to be aimed at refuting Gnostic Christianity — using a lexicon and style that are markedly different from Paul’s as found in the authentic Pauline epistles — which was not extant in the time of Paul, and which would place the text as having been written sometime in the early 2nd century.
You bring up some good points regarding missing events in the book of Acts, and if we had an original copy of the document that reflected the current text, they might be convincing. But that is not the case. As with the gospels, our earliest manuscripts date only to the 4th century, and all of the manuscripts that we have differ from and conflict with one another. And there are other reasons as well to believe that Acts has been compiled from multiple sources and edited far beyond reliability: shifts in perspective, repeated and conflicting accounts of the same events (such as Paul’s conversion), and conflicts with what Paul himself said of his own life and of the early history of the church, as recounted in the epistles. And as well, the Book of Acts ends in triumph, with Paul preaching the gospel in Rome “with all boldness and without hindrance.” Had it ended with the death of Paul, it would have ended in ignominy and defeat.
Likewise with regards to the persecution of Nero. The texts of the New Testament were recorded, in part, with the aim of creating new converts to the religion. A life of brutal persecution would hardly have been a strong selling point, and, being as Christian persecution was largely localized up until the edict of Decian, could have been safely omitted from the text.
We are not certain about the dating of the gospels, or about any of the texts in the New Testament, but at the least, we cannot yet refute the current consensus of late authorship. And if we uncover new evidence that allows us to do so, the gospels will remain historically dubious regardless. Our faith — yours and mine — must either withstand the text, or be defeated by it, but in either case the text is insufficient as justification for the faith.