Ed,
I have no idea on the treason part. As for the pardons, those not covered by the general amnesty who had to apply for a pardon were:

1)diplomatic agents or officials
2)persons who left judicial posts under the United States to aid the rebellion
3)Confederate military officers above the rank of Army colonel or Navy lieutenant
4)members of the U.S. Congress who left to aid in the rebellion
5)persons who resigned commissions in the U.S. Army or Navy and afterwards aided in the rebellion
6)persons who treated unlawfully black prisoners of war or their white officers
7)persons in military or civilian confinement or custody
8)individuals who had absented themselves from the United States in order to aid the rebellion
9)graduates of West Point or Annapolis who served as Confederate officers
10)ex-Confederate governors
11)persons who left homes in territory under U.S. jurisdiction for purposes of aiding the rebellion
12)persons who engaged in destruction of commerce on the high seas or in raids from Canada
13)voluntary participants in the rebellion who had property valued at more than $20,000
14)persons who had broken the oath taken under the provisions of December 8, 1863.