"Deduct from these amounts.......derived from customs...." -- Lincoln Message to Congress, December 1864
The tariff data is incorrect for the purpose you post it.
The President presented the data from the annual departmental report from the Secretary of the Treasury which was cited on your Link.
The "customs" data was computed on gross revenues on all dutible products landing at all tariff houses.
As a matter of procedure, it contained all of the dutible products that were registered upon arrival, including reexport goods that were to be later shipped to other areas such as Central and South America. The Treasury did not subtract re export data, and therefore the information is inflated.
If you want the actual net tariff revenue to the treasury, that was published by the US Customs office. I will be glad to provide it to you if you are interested.
The revenue information corresponds with the figures quoted in the Statistical Abstract, your own source.