1. Shiki was the only surviving witness of the Nanaya massacre and he saw Kouma killing his mother and everyone else.
Shiki is the little boy Kouma talks to in the end of Red Demon God.
Kouma is the monster (Crimson Red Vermillion) that appears in Shiki's dreams in Kohaku's route.
Actually, Kouma is the first character that appears in Tsukihime other than Shiki, because he appears in the opening scene too.
2. You mean when Kouma was a child or in their final showdown?
When he met Kouma as a child, Kiri wasn't in his right state of mind, he didn't even know why he had crushed his eye.
When Kouma became an adult, his eye would probably have the same fiendish invulnerability as the rest of his body.
3. He lived in the Tohno mansion for a while. He was kicked out by Akiha a short time before the beginning of Tsukihime.
Other than that, I don't know.