Right, it needs to be a comma. Otherwise, the わたし immediately after it would refer to the narrator himself and the whole passage would become nonsensical.
Unlike in English, the use of commas is in large part left to each writer's discretion.
Yes, "I've been afraid for seven years, ever since that incident..." is accurate.
Regarding the 頭をひねり, it's saying that the 42/46 incident lead him do two things at the highest level in his life. One is 頭をひねり (racked his brains) and the other 怖い目にあっ た (got treated to a painful experience).
四十二を四十六にした
ＡをＢにする = to make A into B = to fabricate by changing A to B
Literally, take A and pretend it's B.
Finally, I already know how online translation doesn't work. I don't think it ever will between Japanese and English in our lifetime.
