The writ of habeas corpus
The first amendment via suppressing dissenting newspapers
The second amendment via widespread gun confiscation
The doctrine of the separation of powers via harassment of the judiciary
Splitting a state, Virginia, without its consent
Instituting an income tax
Amendments 4, 5, and 6 through the suspension of the civil authority
...and those are just a few of them.
The writ of habeas corpus
A fully justified emergency power, later ratified and authorized by the Congress
The first amendment via suppressing dissenting newspapers
It is often alleged that Lincoln violated the "prior restraint doctrine" of the 1st Amendment. In the few cases where newspapers were closed or presses destroyed, there existed evidence of collaboration. And these cases were relatively few. If the "freedom of the press" had been "suspended," how is it so many newspapers opposed to the Lincoln administration continued to operated openly and freely?
The second amendment via widespread gun confiscation
You can take guns away from enemy combatants and civilians in a war zone. It is a prudent measure. Nobody in a state that had purported to secede had any Constitutional rights.
The doctrine of the separation of powers via harassment of the judiciary
From what you have posted, the only judges temporarily detained attempted to "dictate" to a co-equal branch of government. Even in 1861, the Jacksonian view of the Constitution allowed for each branch of the government to come to their own interpretation of the Constitution in the absence of an authoritative interpretation. As it was, Lincoln lawfully suspended the habeas privilege as a war time necessity, and the judges overstepped their jurisdiction.
Splitting a state, Virginia, without its consent
The loyal people of "western Virginia," finding themselves in an area with no recognized government, petitioned the Congress for statehood.
Instituting an income tax
Found unconstitutional many decades later, but not a "suspension" of the Constitution! (You're reaching now.)
Amendments 4, 5, and 6 through the suspension of the civil authority
The establishment of military rule and military tribunals in war zones was approved by the Supreme Court. Where the Court later found military tribunals operating in areas they thought unacceptable, the tribunals ceased. Again, no "suspension" of the Constitution.
...and those are just a few of them.
Yada, yada, yada.