1)
From where did the voice come?
1.
Rashi (3): It came from the Kodesh ha'Kodoshim. This was from Eli's direction, for the Kohanim guarded inside, and the Leviyim, outside (Midos 1:9). Verse 3 is written out of order, so "va'Yikra Hashem" will be next to "Heichal Hashem", to teach that the voice came from there.
2)
Why did Shmuel say "Hineni"?
1.
Malbim: He assumed that Eli had called him. He wanted him to know that he (Shmuel) is not sleeping.
