Dear Mike:
You have made quite an impressive list. Since I am marginally familiar with the Qur'an (in English paraphrase) I can attest to the general thrust of your list. But why should Muslims feel apologetic for anything which you have listed here? IMHO, no Muslim should feel ashamed of anything which is written in the Qur'an, just as no Christian or Jew should be ashamed of anything in the Old or New Testaments.
We Christians should be not be so ready to condemn the faults, whether real or imagined, of other religions, including their inspired writings. We have much to answer for from our end. The Christian Bible contains many questionable ideas, but this does not mean that the Bible is an invalid revelation from God.
Many Qur'anic references on your list pertain to the Last Day and to the fate of unbelievers. Why should that be so terrible to contemplate? Are you scandalized that most Muslims believe that Christians will go to hell? It doesn't really bother me: if it happens, I am sure that I can handle it. Sure wouldn't be the worst possible outcome.