Hello Sandra-
I have been following the thread of your search for Capt. Smith and although I don't have anything to add to assist you at this point, I was wondering if you might clarify a question I have...

In your initial post you indicated that you had located Capt. Smith in the 1880 census and that is the last you heard of him and that he probably d. 1880-1900 because his wife Jeanette was widowed by the 1900 census. These death dates also seemed to be confirmed because he had not accompanied her when she and son Joseph relocated out west.

Was the 1880 census you referred to the one where Capt. James P. Smith was residing with the the McDole family in Chicago?
If so, I found the transcription (I haven't seen the original) of that 1880 census on the LDS (familysearch.org) website. Assuming this is, indeed, your Capt. Smith and the transcrition is accurate, I note that his marital status is listed as "divorced" in 1880. If he was divorced from Jeanette in 1880 couldn't this account for the fact he wouldn't have accompanied her when she journeyed west? It does appear that he was living in Chicago without Jeanette with the Capt. David McDole family in 1880.
I couldn't locate your Capt Smith either after the 1880 census, but I was wondring if perhaps looking into the McDole family and attempting to ascertain what (if any) relationship they had with your Capt. Smith might assist you in your search for him. I can tell you that Capt. David McDole (b. ca 1828) died in Chicago in 14 April 1898 and is buried at the Oak Ridge Cemetery.
Have you come across the McDoles in your search for your Capt. Smith?
Just a thought....
Paul