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unconditionally, and without reservation, to all and every person who directly or indirectly participated in the late insurrection or rebellion, a full pardon and amnesty for the offense of treason against the United States, or of adhering to their enemies during the late civil war, with restoration of all rights, privileges, and immunities under the Constitution and the laws which have been made in pursuance thereof.

Yet I've heard repeatedly of long periods during which the franchise and other civil rights were denied to leading Confederates in the reconstructed South.

Do you know which story is correct?

Sherman Logan: "Yet I've heard repeatedly of long periods during which the franchise and other civil rights were denied to leading Confederates in the reconstructed South."

I can't cite many specific examples, but possibly we're talking about Federal law on treason, versus reconstruction era state and local ordinances.
Confederate officials pardoned for treason might still face laws which prevented them from holding offices in the post-war government.

However, one example which does come to mind is Lee's Lieutenant, James Longstreet, who settled in New Orleans after the war, and was appointed to various government positions, including adjutant general of the state militia and by 1872 a major general in command of all militia and state police forces within New Orleans.

All this for a man of whom President Johnson said,

"There are three persons of the South who can never receive amnesty: Mr. Davis, General Lee, and yourself.
You have given the Union cause too much trouble."

But, Regardless of President Johnson's opposition, the United States Congress restored Longstreet's rights of citizenship in June 1868.

And I'm certain a little research could dig up a list of Confederate generals & others who returned to Congress, became their states' governors, etc.
So my overall impression is that former Confederates were readmitted to citizenship pretty much based on however much they desired it.

But Lost Causers who told the world:

"I won't be reconstructed and I do not give a damn,"

were mostly left alone to stew in their own juices, just as they are today...

;-)