Thanks for your post... but I think you may be taking too much of a literal interpretation of what Qur'an is really saying and ergo is not so contradictory as you may be suggesting....and you therefore have overlooked the possibility that both can be true.
When the Qur'an is reporting the crucifixion I believe it refers to the Spirit of Christ that cannot be crucified or killed. So in this way there is no real contradiction:
and their boast, "Behold, we have slain the Christ Jesus, son of Mary, [who claimed to be] an apostle of God!" However, they did not slay him, and neither did they crucify him, but it only seemed to them [as if it had been] so; and, verily, those who hold conflicting views thereon are indeed confused, having no [real] knowledge thereof, and following mere conjecture. For, of a certainty, they did not slay him:
Qur'an 4:157
"...but it only seemed to them [as if it had been] so.." They believed they had killed the Cause of Messiah but they were wrong...
"...nay, God exalted him unto Himself - and God is indeed almighty, wise."
Qur'an 4:148
Jesus committed His Spirit to God.
So there is not so much a contradiction as you suggest I believe.