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cowboyway: "A general amnesty was issued by Johnson but Davis was still under indictment.
The Supreme Court just let it die without issuing a formal order of dismissal."

No, Davis was indicted for treason in 1865, served two years in prison, released on $100,000 bail paid by prominent northerners.
His federal case came to trial in December 1868, in a district court headed by former Ohio governor and Lincoln Secretary of Treasury, Justice Salmon Chase, then acting as circuit judge, and Chase favored dismissal of the charges.
After preliminary arguments, President Johnson issued a pardon covering Davis, December 25, 1868, following which the court case was dropped.

My opinion is that Davis & other Confederate leaders could have been convicted of treason, with some courts & judges, but not with others.
Seems to me Johnson's pardons worked out best for all.

The only thing that has ended about The Civil War is the shooting. I wonder about that sometimes.

You're dodging the point (as usual). The point is that the federal government didn't want a trial. And why not? Because it would have exposed disHonest Abe as the war criminal that he was and would have upheld the right of secession.

President Johnson, Lincoln's successor, thought the easiest way out would be to pardon Davis, as he had pardoned many other Confederates. But Davis refused, saying, "To ask for a pardon would be a confession of guilt." He wanted a trial to have the issue of secession decided by a court of law - where it should have been decided to begin with - instead of on battlefields. Most Southerners wanted the same.

Also read: The Trial of Jefferson Davis, An Interesting Constitutional Question