しか does get a negative verb at the end while maintaining a positive meaning.
There is a pattern: しか＋ないverb meaning "only something" (positive sentence). eg:
この学校で田中さんしか知らないです。- I only know Tanaka-san in this school.
朝ごはんは、トーストしか食べなかったんですよ。- I only had a toast for breakfast.
For further reference.
So if we breakdown the sentence
学校へ is taking the verb 行っていません, but since it is inside the aforeamentioned "しかない pattern", it becomes only go / only went. わずかに purpose here is to only serve as an adverb for the verb 行く. Therefore:
I only went to school for barely two months.
3 - Yes, it would mean something like "I did not go to school for barely two months" / "I haven't been to school for barely two months"
forth second question:
It can mean that when you haven't done something in the past, but it is always in the negative tense, and you gotta be careful to not mistake it with
I made the same question some years ago, and the answer was something like this:
見てない also has the meaning "Someone doesn't(has not) see(seen) something ", but the nuance of "ever" is less. See the full answer.