Sorry, don't mean to sound cavalier, but this cracks me up. Whoever wrote it... was s/he a physician? You've done a great job translating so far, both Martin and the helpers that came along. I would try printing it out and using a pencil to see how best to connect the "dots". In fact, maybe I'll use the snipping tool, blow it up & try it. I'd almost say that one part would make sense if it said "had children", but there's no doubt that word is "Calligan." My guess is that the "had" is a form of "nee" perhaps, and Mary was born a Calligan. I don't think they were into naming children by last names as much then, so doubt that John & Mary "had Calligan". Also, it appears there's a period after the "had" (or whatever it is, so maybe it's short for something.
The last sentence of the 2nd part looks like it might begin with "Krause" again? Anyway, I'll print it out and work on it for fun.