
Lisa, as a result of the earthquake in 1868 (and except for the fire of 1906, it was a doozy!) both Mary and her kids went to Alameda. Annie went also.
They lived for that short time, according to John's Journal (and you must sift through that because it took a lot of imagination for him to compile), "in a large rustic holding as a hostelry." It was owned by a Doctor Lambert. According to an 1880 census record a Bernard Lambert lived on High Street in Alameda and he was a retired physician.

Sandra, I had been in correspondence with a person that indicated she was a daughter-in-law of John Amos Gaffigan for a while, and then it ended when the bubble was busted up, and she had to attend to her children. It seems that she had a "Journal" and you had to read it with quite a bit of salt because it was after the fact and did not relate to a lot of real world. But, it contained enough to look around San Francisco and I have used it as a starting point in many of my searches. Aggie B, my grandmother, evidently did not get along with John her father and was very closed mouth about the early years. Actually, very little in that family could have been civil discourse for John went a little batty in his mid-life and later.
I never heard about the Thomas Campbell, but then I actually heard little about that part of the family. His journal did not mention those children and he did mention the Crennan girl, who he married in later life.
I have Charles Campell/Camppell working as a collar maker, not an engineer or commission(?), and as it was transcribed to me it was a Campbell. His Journal stated about 1867, "We are sent to a childrens scholll at No 1 Thompson Ave. More to lose our brogue than anything. There was six houses on this little street. No 1 by Mrs Kelly and her daughter who kept the little school #2 by the Crenan (sic) family - 3 by the Driscoll family 4 - by Mr Goodenough and wife - 5 by Miss Annie Amos and 6 by Mr. and Mrs Campbell..." There was no Thomas Campbell on that street at the time Mary came to live with the two sisters.
But, I do think that you may have found an entry that could lead to some place. That was the "Ames" one. The age does track a bit for Isabella as she was 2 years younger than her sister Anna. Given that she had listed her age as 22 in 1853 she would have been born about 1831 or 1832. Because there may have been something (

) going on between the McCarrolls and the Amos girls, and she left for Philadelphia from Londonderry (Moville?) that is a port in Ulster and closely associated with those of Tyrone. We have never been able to track those girls, only Mary and Patrick and the fact that they were both born in Ireland.

Could there have been something about Connecticut? Mary and the kids stayed there, according to the Journal, before they left for California. Or, alternatively, because this person came through Philadelphia (and a lot of Irish did), she may have gotten married around there. Could Anna have been married to someone there, or over in Ulster - we may never find out.
Just remember, in Latin the term for Irish was Scotus. And it is just across the lake, and a lot of Irish had gone over there, and a lot of Scots had come over to Ireland and Ulster over the years.
Thank you, thank you! Jim