You said "In 1898 the U.S. Congress removed the following Section of the 14th Amendment.."

Congress does not have the power to remove a section of an Amendment. An Amendment can be amended or repealed, as section 1 of the 14th was to allow 18 year olds to vote, but it is subject to the amendment and ratification process.

The 14th Amendment, from its inception, allowed Congress to remove the disability regarding insurrection/rebellion for an individual or group by a 2/3 vote - as it did in the various acts you cited, but section 3 itself is still the law unless Congress has specifically removed the disablility from a given individual or group. Section 3 would not have applied to persons pardoned prior to the 14th Amendment's ratification because of Article I, Section 9's prohibition of ex post facto laws.