Let me begin by thanking you for pointing out my glaring error that the argument stems not from Article 2, but Article 3. I apologize for that mistake.
Section 1 vests the Judicial Power in BOTH the Supreme Court and the inferior courts. The subject "judicial power" acts through the verb "vests" on both objects "Supreme Courts" and "inferior courts". It can be read, as I believe you read it, to be one power, divided or shared between the two courts. I read it to vest completely the Judicial Power in each court. A great argument to counter my own interpretation is that Article 1 vests the Legislative power in the Congress, but we know the Senate and the House have divided roles.
Ultimately, history supports your interpretation. Additionally, you are correct that inferior court is not well defined. But, your position is strengthened by the word inferior itself. How could a court hold equal power with the Supreme Court and remain inferior? Under my interpretation, inferiority refers to subjugation of the lower courts by decisions of higher courts. Once again, though, the practices immediately following the Court's founding and its modern practices as well do not support my position.
Despite all of this, I believe that "special courts" created by Congress violate the spirit of the Constitution, because they effectively hand off legislative decisions to the "special courts" and give them the effect of judicial decisions. Ultimately, for me, this is a separation of powers issue. Again, though, an argument for the spirit of the document is weak when up against its own words and people who have acted consistently with your interpretation.