How can you be sure that the quotes in the gospel attributed to John are accurate? did he memorize everything Jesus (pbuh) said? the people may have thought Jesus (pbuh) died, because he passed out, it even tells us that in the Qur'an:
004.157
YUSUFALI: That they said (in boast), "We killed Christ Jesus the son of Mary, the Messenger of Allah";- but they killed him not, nor crucified him, but so it was made to appear to them, and those who differ therein are full of doubts, with no (certain) knowledge, but only conjecture to follow, for of a surety they killed him not:-
PICKTHAL: And because of their saying: We slew the Messiah, Jesus son of Mary, Allah's messenger - they slew him not nor crucified him, but it appeared so unto them; and lo! those who disagree concerning it are in doubt thereof; they have no knowledge thereof save pursuit of a conjecture; they slew him not for certain.
The Qur'an tells us Jesus (pbuh) was not killed. For someone to be killed they are dead, and never return.... I understand that the Qur'an says he was not dead, which is true even if you believe in the resurection, indeed you even agree he was alive and is still alive, hence he has not been killed and is not dead. He is waiting in the heavens to complete his role as messiah and save us all in the last and greatest fitna, the fitna of Dajjal.
So there is the reason people thought he was dead, i can see two possible explanations. The Qur'an may be saying that those who thought they slew Jesus really believed he was dead, and didnt know that he was still alive.... (this is only a theory brothers and sisters im not saying i believe the following) or it could be the fact that Jesus (pbuh) may have been in a state like death, where his heart had stopped, so you could declare him medically dead, but came back round (resurected) and hence the ayat is still true, the people thought they had killed Jesus (pbuh) but they hadnt really killed him because he was still alive.
Back to my original point, you dont know how accurate these quotes are, you dont know how the book was collated, you dont know what sources went into their creation, alternative motives, poor character, even poor memories! I haven't seen evidence from within the four gospels that they are divine, and when you compare these texts with Qur'an, they really arent even a millionth of the standard of the Qur'an, really even a genius in literacy couldnt reproduce something that amazing.
I understand what you mean when you say the fundamentals are the same, and of course they are if the fundamentals were contradictory they wouldnt be in the christian doctrine would they!! their stories corroborate, but that doesnt tell us that they are 100% accurate. it doesnt mean everything they say is true, how many times does Jesus (pbuh) say in the gospels he is the son of God? we will never truely know if Jesus (pbuh) said these things until he returns, but for me there is a lot more evidence to suggest he isnt, from the old testament, the new testament, and the Qur'an.