Your first question is, how can the Vedas be considered eternal since they contain many historical references? But history is also eternal. For example, six months ago there was summer now there is a new season, and in another six months summer again. This calculation of one year is history but the summer and winter seasons are also eternal. There is a saying, "History repeats itself." Why make a distinction between history and eternity. Things are happening eternally; this is history.
You have asked why the four Vedas are written in a different type of sanskrit from classical. This is not extraordinary. In India, sanskrit pronunciation is different in the North and South, and there are many different dialects. So the Vedas may also be presented with some differences within.
You have further questioned how the Vedas can be 3,000 B. C. in age. Modern historians cannot pick up when the Vedas came into existence. From our historical references, however, we understand the Vedic knowledge has been current since the time of creation but the knowledge was originally accepted in disciplic succession from spiritual master to disciple. Later, when Vyasadeva found the peoples' memories decreasing he wrote it into language. Otherwise it was existing by sruti, or hearing. So when this hearing began there is no history. He simply recorded the sruti, and there is no question of change. We have to understand Vedic knowledge on the authority of the disciplic succession not from mental speculators who are simply rascals and have no entrance into the Vedic knowledge. You mention Sankara, but Sankara hid so many things, so it is no wonder he did not mention Bhagavatam. There are great authorities of Bhagavatam and it is they we have to follow.
Similarly, the Bhagavatam is mentioned in an earlier Purana means that the whole language is sruti. Although the Bhagavatam may not have been written the tradition was there. It is written by Sridhara Swami quoting the Puranas, that the practice was to write out the Bhagavatam by hand and present it to a learned man.
The Bhagavatam we have is the same Bhagavatam. It was originally spoken in four slokas by the Supreme Personality of Godhead to Lord Brahma. All these descriptions are in my books and I request you to read them very carefully as you are a learned scholar. I appreciate your humble attitude, and I have a good report of your activities from Jagadisa prabhu. Please go on increasing in Krsna Consciousness and you will find all spiritual understanding and happiness not only for you, but for whomever you meet.