[Non-Sequitur]

What took the Feds so long? Why didn't they rule during the war against Lincoln's use of the military against Northern civilians?

The court only rules on cases which appear before it. Prior to Milligan no cases had been appealed to the Supreme Court.

It was legal for the Confederate Congress to do that. Besides, there was fighting throughout much of the South. The North, on the other hand, had vast areas that were not being invaded.

It was legal for the U.S. Congress to do so as well. The Constitution places no such limitations on the suspension. The difference is that the Supreme Court determined that public safety required a functioning judiciary to preserve it and so long as one existed and was operating freely then the suspension wasn't necessary. The confederate suspension occured long before Union forces appeared in most of the confederacy, yet the suspension was in place in those places and there was no confederate institution that could challenge that. Southern civil rights effectively died from Key West to Nashville, El Paso to Norfolk.

[rustbucket]

Habeas corpus cases did get review:

The Courts and Judges of the States have concurrent jurisdiction with the Courts and Judges of the Confederate States in the issuing of writs of habeas corpus, and in the enquiring into the causes of detention, even where such detention is by an officer or agent of the Confederate States.

The courts of this State, as well as the individual Judges, have jurisdiction to issue writs of habeas corpus and to have the return made to them in term time and, as a court, to consider and determine of the causes of detention.

This was from: State review of habeas corpus

Also, I found the following in The Weekly Mississippian (Jackson, Mississippi) of Aug 21, 1861:

The Confederate States' Courts

The Confederate States Supreme Court, says the Richmond Examiner, will hold no session until it shall be organized under the provisions of the Permanent Constitution. Under the Constitution of the Provisional Government, it was provided that the Supreme Court shall consist of all the District Judges, and shall sit at such times and places as Congress shall appoint. Under the Permanent Constitution, however, the Supreme Court has not been established; and during the existing hiatus in our judiciary system, the clerks of the District Courts are empowered to issue writs of error, with the same force and effect as issued out of the Supreme Court, and returnable on the second Monday of its first term after its establishment.

Did Jefferson Davis overrule or ignore Confederate courts on habeas corpus cases?

[GOPcapitalist]

there was no confederate institution that could challenge that

That is false. Throughout the war cases that would have likely been material for a national supreme court went to the respective state supreme courts.

[rustbucket]

It was legal for the U.S. Congress to do so as well. [suspend habeas corpus]

Correct, but Lincoln didn't have that power. Again I ask, if Lincoln had the power to suspend habeas corpus in 1861, why did Congress feel they had to authorize him to do so in 1863?