What is a Muslim's position when clear Quranic verses, such as those concerning shortening the prayer, the Hadd (punishment) for adultery, and forbidden foods, contradict scholarly fatwas that seem to oppose them?

The sources of rulings in Islam are the Quran and the Sunnah, and the Sunnah is a proof by scholarly consensus.

Shortening prayers (qasr) is a charity from Allah, established by the pure Sunnah through the words of Umar ibn al-Khattab, may Allah be pleased with him, when he asked the Messenger of Allah, peace and blessings be upon him, about shortening prayers during times of security. He informed him that it is a charity from Allah.

As for stoning (rajm) for the married adulterer, it is established by the Quran, whose recitation was abrogated, and by the Sunnah, as mentioned in the hadith of Umar ibn al-Khattab, may Allah be pleased with him, regarding the verse of stoning, and the hadith of Ubayy ibn Ka'b, may Allah be pleased with him, regarding the verse of "the old man and the old woman."

Regarding the prohibition of certain things not mentioned as prohibited in the Quran, the Sunnah prohibits domestic donkeys, every beast of prey with fangs, and every bird with talons.