What is the etymology of the expression "so far, so good"?
Why is the meaning of "so far" in that phrase different from the meaning it has in "it's so far"?
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This is an older meaning of "so" that used to be very common in English but has fallen out of use, where "so" means "in this manner/condition". We still use it when we say things like "you do it like so", "just-so story", "it was so long (and you gesture with your hands to indicate out long)". Actually, the first three entries in dictionary.com seem to convey this meaning.
So, the "so far" part means "up to now" and the "so good" part means "it is good in this manner/condition".
I don't know what the etymology is, but the way I interpret the saying, the meaning of "so far" isn't so far from the meaning you refer to, the critical difference being that in your example "far" is referring to physical distance and in the saying "far" refers to length of time.
One of the meanings of the phrase "so far" (always with the stress on the "so") is "up to now", with an implication that whatever (good) state of affairs is being described may not continue: "So far I haven't had any problems"
"So far, so good", like many proverbs, is made up of two abbreviated phrases set against one another. It means "Up to now, everything is good".
I can't think of another context in which "so good" has this meaning.