Stephen,

"The 14th amendment could not punish the Confederates due to the rule of Ex Post Facto."

Sorry, but that is wrong...at least according to everyone involved in the Davis case. Davis' defense attorneys argued that the 14th amendment punished him, the Chief Justice of the Supreme Court agreed that the 14th amendment punished him, and even the prosecution acknowledged it but argued that it wasn't enough.

In short, NO ONE involved in the Davis case believed your legal argument above.

Now, if you still believe there was some vast coverup (which I don't see how there could be), and that Chase and Davis' attorneys used the 14th amendment as an "excuse" to drop the case, you'll have to provide actual evidence.