The Journal of the Assembly lists the totals as 65,013 for Machin and 43,893 for McKinstry.
There were no votes from Lake County listed on the statewide abstract. In addition to the regular county vote, the Soldier vote was 4,199 for Machin and 106 for McKinstry.
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, "Lt. 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)