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JayJoe-Nice theory, but there was only one San Francisco team in 1889(Lew's book was wrong). The 1889 League was composed of Oakland, San Francisco, Stockton and Sacramento. So, if one was to speculate the question would be where are the Stockton players. What makes their omission all the more unusual is that Stockton was the 1888 League champion.
Richard--In answer to your question, if one were to assume that a full sheet of California League players was produced then there would be five players still unaccounted for. Let me offer another theory. Goodwin originally planned to produce a sheet of 24 which was to include five Stockton players. For some reason the Stockton glass plate negatives did not arrive on time, or arrived broken(not hard to envision for pieces of glass being shipped cross country) so Goodwin produced a partial sheet of only 19 cards representing the players from the other three teams.