Is it really rationalism?

The complaint against the ordination of Gordon Clark to the Orthodox Presbyterian Church in 1944 consisted of four theological issues (The incomprehensibility of God, divine sovereignty and human responsibility, the faculties of knowledge, and the Free Offer of the Gospel ) but underlying these issues was a single concern; one of hermeneutical method.
The method of Gordon Clark was called “rationalism” by the complainants. Yet, it is clear that Clark from his many writings against rationalist philosophers is not to be accused of philosophic rationalism; i.e. beginning with reason as the chief source of knowledge to man.  On the contrary, Clark’s philosophy, later called Scripturalism, rested on the Scripture alone as the single presupposition to make knowledge possible. He critiqued rationalism in “Three Types of Religious Philosophy” and the rationalist philosophers (Plato, Descartes, Hegel) repeatedly through his works.
Clark believed from Scripture that “God is not the author of confusion” and that the Scriptures were revealing something, not nothing. Thus, where Van Til and the complainants saw unsolvable apparent paradoxes in Scripture, Clark was willing to test that claim.  He was willing to use the method he thought proper to attempt solutions.
There are two questions that must be considered regarding the teaching of apparent paradox in Scripture.
The first question is “to whom are these paradoxes apparent?” Is it not the case that each person sees various amounts of difficulties in Scripture?  Where the new believer may be thoroughly confused and see many paradoxes, the learned exegete knows the solution by comparing Scripture with Scripture.  It was this method, comparing Scripture with Scripture that Clark argued in favor of.  To my knowledge it is a standard method in hermeneutics.
Even the complainants surely would have agreed that some apparent paradoxes have been resolved.  How then, without knowledge of such, can it be claimed that other apparent paradoxes can’t be solved? Consider that the Lutheran Church – Missouri Synod believes that the question of “why are some saved and not others” known as the “crux theologorum” is an apparent paradox.  But, Van Til, being unabashedly Calvinist has solved this apparent paradox with the standard TULIP formulation. Why is it here acceptable for Van Til to solve a paradox, but not for Clark to do so elsewhere?
The second question is, how do you know that Scripture teaches that God presents paradoxes which we cannot solve?  Does Scripture teach that there are such paradoxes?  I’m unaware of such a teaching.  Perhaps it exists; I’d be glad to be enlightened.  If Scripture teaches such paradox is this teaching itself a paradox not to be understood?
Surely, not all attempts to solve apparent contradictions are valid.  It was not that Clark had solved the paradoxes incorrectly that the Complainants were arguing about; it was that he tried to solve them at all.
But we have a method for understanding Scripture as given in the Westminster Confession of Faith.  The confession tells us that we can have knowledge of such that is “by good and necessary consequence” derived from Scripture.  Deduction is surely meant by “good and necessary consequence.”  And it was the method of deduction, when properly used, which Gordon Clark supported. Otherwise, where is the line to be drawn?  Who determines what is unsolvable or irreconcilable?
In a collection of articles by Herman Hoeksema collected in the “Clark – Van Til Controversy” he asks “Is it really rationalism to attempt to bring Scripture in harmony with itself?”
Is it really rationalism?  Is there a better hermeneutic than to compare Scripture with Scripture?  Is deduction by good and necessary consequence an improper method?
I think not.