| Recap of the Popular Vote
At the end of the popular election, 88 Madison Electors had been chosen, compared to 16 Pinckney Electors. While it was a large margin for Madison, Pinckney had scored a net of 14 electoral votes. Madison was one electoral vote shy of a majority.
Legislative Selection of Presidential Electors
Seven state legislatures chose Presidential Electors in 1808. Madison was assured of 16 additional electoral votes, and Pinckney was assured of 31. Their totals thus stood at Madison-104, Pinckney-47, undecided-25.
The more important of the two undecided states was New York. The legislature was badly divided, being roughly 45% Federalist, 35% Clintonian, and 20% Madisonian. At first, the Federalists sought to vote with the Clintonians, but the latter were not interested. The DRP Caucus met on 11/6/1808 (New-York Gazette General Advertiser, 11/8/1808) and adopted a list of 23 suitable candidates for the 19 positions: 15 Clintonians and eight Madisonians. The following day, 11/7/1808, the legislature elected 16 Clinton Electors and three Madison Electors (Republican Watch-Tower, 11/8/1808). The vote was 65 for the DRP slate to 46 for the Federalist slate. The initial report was that the three Madison Electors would support Clinton out of respect for him.
In Vermont, the legislature was almost evenly divided between the two parties. When the vote for Presidential Electors was cast around 11/20/1808 (reported in the Albany [NY] Register on 11/22/1808), Madison's Electors carried the day by eight votes.
As a result, the nationwide electoral tally stood at Madison-113, Pinckney-47, and Clinton-16. DRP leaders around the nation were disgusted at the decision in New York State, and they wrote letters to the Electors there and urged them to support Madison instead of Clinton.
Casting the Electoral Vote
The Presidential Electors met in their respective state capitols on 12/7/1808 to cast the electoral votes. One Madison Elector in Kentucky was unable to attend due to illness, so that one vote was lost (Kentucky did not have legislation allowing the remaining Electors to fill vacancies). In New York State, ten Clinton Electors voted for Madison. The final result was Madison-122, Pinckney-47, Clinton-6.
Clinton supporters in New York State were furious at the defecting Electors there. The NYC newspaper the American Citizen, in its report of the casting of the vote on 12/12/1808, gave the names of the six Clinton Electors, who had "represented the will of the state of New-York and of its Legislature, in voting for George Clinton for President."
The result of the vice presidential race was not identical to that for President. Madison Electors in VT and OH chose not to support VP Clinton for re-election because he did not abandon his campaign after losing the national DR Caucus. Instead, they voted for John Langdon. Clinton was still re-elected, receiving 113 votes. The six Clinton Electors cast 3 votes for Madison and 3 for Monroe.
The Joint Session of Congress
The electoral votes were counted before a joint session of Congress on 2/8/1809. The vote was counted in the U.S. House chamber. Just prior to the arrival of the Senators, the issue was raised that the Speaker of the House preside over the counting of the vote. The measure was introduced as an insult to VP Clinton, due to his intransigence in continuing his independent campaign for President while at the same time campaigning on the winning ticket for Vice President. The difficulty was resolved when Clinton did not appear for the count. John Milledge GA, the president pro tempore, instead presided. (National Intelligencer, 2/10/1809). The tellers were U.S. Senator Samuel Smith MD, U.S. Rep. Wilson C. Nicholas VA, and Nicholas Van Dyke DE.
The reading of the certificates of vote took about two hours. At the end, U.S. Senator James Hillhouse (F-CT) mentioned that one certificate was not signed by the governor of its state (though he did not identify the state), but the assembly took no action on this piece of information. Sen. Milledge declared Madison and Clinton to be the President and Vice President elects, and the joint session came to an end.
Popular Vote of 1808 | 
122 (69.71%)