Find the earliest. The first time we hear about an upside-down crucifixion is in the apocryphal Acts of Peter written about 170 - 190 AD. That is where the myth got started.
2. There weren't quite a few. There were none. If the Jews were chased by force out of Rome and the Christians were illegal, there weren't any, at least operational.
What does it take to operate a cemetery --- a shovel? And look on a map sometime of Rome and see all the Jewish cemeteries --- I wonder how ancient some of the old grave markers are?
Jews who were Roman citizens, like Paul, could still enter or remain in Rome even after Claudius's decree, but those who were not citizens, like Peter, would not even be permitted to enter. In the Book of Acts Paul meets with a group of Jewish elders when he arrives there in 60 AD. These must have been part of that community of Jews who were permitted to stay in Rome.
I see. Anything that was written by the Church Fathers that supports your arguments is to be accepted as, well, gospel, and anything which doesn't is myth.
It takes more than a shovel to operate a cemetary. And wondering about the age of various cemetaries does nothing to make the point.
Yes, there was a small Jewish community in Rome, but remember that Paul was arrested immediately after entering Rome, that he spent his time preaching and converting as many as he could. Christians were being killed outright. Paul wouldn't have been considered a religious Jew at that point and Peter would not have been either. Remember too, that the Jews that were there wanted him arrested.
Therefore: no burial would have been available for Peter at a Jewish cemetary. Christians didn't have any. He had to have been buried in a pagan cemetary. QED.