I've been to San Francisco, I've been to Dr. Lane...

Levi Cooper Lane (1828-1902)

Dr. Lane didn't leave the U.S.Navy until 1859; then relocated to San Francisco in the early 1860s. His own clinic didn't really get up and running until the 70s. Note: The modern versions move him back east somewhere.

What is the earliest actual example in the document record or is the 1856 date just from the lyric?

"Out of fix" is out of square, not flat or true. But then there is no such thing as a 't-planch' (t-plank?) or 'dusting out' that I'm aware of either. Lot's of modern variation on that lyric too.