No, you are the one who is incorrect. Article I is silent on who may suspend habeas corpus. It only covers the conditions under which it can be suspended.
Alternatively, a lower federal court can settle the matter of constitutionality so long as its ruling is not appealed.
No, a lower court may determine constitutionality if the Supreme Court declines to take their ruling under consideration. At that time, the lower court decision is accepted as the opinion of the Supreme Court.
No, the lower court (say 2nd Circuit) determines the constitutionality of a law within its own territorial jurisdiction. Such never becomes accepted as the opinion of the Supreme Court by denial of cert. If a court from another jurisdiction (say 9th Circuit) rules differently, the Supreme Court may decide to rule on the issue and resolve it.
When a lower court decision is not appealed to the Supreme Court, or cert is not granted, the lower court decision remains the precedent for that territorial jurisdiction but is not binding as precedent on any other jurisdiction as is a Supreme Court decision.
"All legislative Powers herein granted shall be vested in a Congress of the United States" - Article I, Section 1, opening line.
Now what was that you said about Article I being silent again?
Wrong again. Circuit Court decisions are binding in their jurisdiction as long as they are standing (and in this case the Merryman ruling was indisputably within Taney's circuit jurisdiction). That means they remain in effect as long as (a) the Supreme Court does not take up an appeal AND overturn the circuit ruling, or (b) the losing party opts against appealing the decision and permits it to stand. With Merryman, Lincoln's intentional act of ignoring the ruling may be considered as opting against an appeal. Thus he is bound to abide by it.