Why does it say "Al Shafan"?
Radak: This is like El Shafan. Also "va'Yelech Elkanah Al Beiso" (Shmuel I, 2:11) is like El Beiso.
Where did he find the Torah?
Rashi, Radak: It was under a row of rocks. It was hidden when Achaz 1 burned the Torah.
Radak: It was in its place, next to the Aron. So it says in Divrei ha'Yamim II, 34:14 - "when they were taking the money out of Beis Hashem, Chilkiyah found the Sefer Torah. Malbim - it says Sefer ha'Torah; the prefix Hei shows that it is the special Sefer, that Moshe wrote. In Divrei ha'Yamim, it says "b'Yad Moshe."
Radak: This is difficult. Refer to 22:8:3:1. Alei Tamar (Shabbos 16:1) - Rashi and Radak cite a Midrash that we do not have. Sanhedrin 103b says that Achaz sealed (stopped study of) Torah, and Amon burned the Torah. Ya'avetz (on Seder Olam 24) fixes the text of Rashi to say Amon. Targum Rav Yosef on Divrei ha'Yamim II, 34:15 says that the Sefer was found Ganun (or Ganuz, i.e. hidden).
Why was the Torah a Chidush to Chilkiyah and others? Menasheh did Teshuvah when he was exiled to Bavel (Divrei ha'Yamim II, 33:12-15). He returned to Yerushalayim, removed the idols and told Yisrael to serve Hashem. Why did he not return the Torah?
Radak: Perhaps Menasheh was exiled in his old age, and did not live long after he repented 1 . He eradicated idolatry, but did not put to mind to seek the Sefer Torah. Yoshiyah was six in the [last] days of Menasheh, and had not learned Torah yet.
Refer to 22:8:3:2.
QUESTIONS ON RASHI
Rashi writes that the Sefer was hidden when Achaz burned the Torah. After Achaz, Chizkiyah spread Torah (Sanhedrin 94b). Why did he not take the hidden Sefer? And when Chizkiyah died, he left many Sifrei Torah!
Radak: Menasheh was king for 55 years. He made Torah forgotten; people turned to idolatry and Nochri rituals. Now, Yoshiyah commanded to look for every place that needed fixing, and to take out the money brought to Beis Hashem. They found the Sefer Torah next to the Aron (refer to 22:8:2:2). They read it, and found that the Torah forbids all the bad things that Yisrael were doing.
Perhaps indeed, there were Sifrei Torah. They were alarmed to find the Sefer next to the Aron rolled in the middle; it should be rolled to its beginning. They found that it was open to the curse that the king and nation will be exiled. This aroused them to realize that they had sinned, and to repent. (PF; perhaps this is Malbim's intent.)
