The Journal of the Assembly lists the totals as 64,323 for Low and 44,492 for Downey.
There were no votes from Lake County listed on the statewide abstract. In addition to the regular county vote, the Soldier vote was 4,159 for Low and 140 for Downey.
Candidates' party affiliations obtained from the 9/1/1863 Sacramento Daily Union. https://www.cdnc.ucr.edu/?a=d&d=SDU18630901.2.3.2&e=-------en--20--1--txt-txIN--------
Source for Popular Vote data: California State Archives, "Governor," Statement of the Votes Polled at a General Election Held in the State of California on Wednesday the Second day of September A.D. 1863 (Sacramento, 1863)