The "clues" I refer to are of two kinds: linguistic and numeric. The linguistic clues were there to be seen, but wouldn't readily be recognized for what they were. One such type of linguistic clue was what I call "catchword at a distance". Conventional Thomas commentators know about catchwords, but they're defined as words occurring in two adjacent sayings (or sub-parts of one). In the world of private Thomas, however, catchwords also exist between non-adjacent sayings. The reason for this was that the "insiders" weren't intended to just read the sayings, but to do something physically with them - things like rewriting them, adding to or deleting from them, changing their position, etc.
With respect to the numeric clues, they're of various kinds, but the most common is simple letter-counts. There can be no doubt that the composers of Coptic Thomas were numerically knowledgeable folks who counted things, most notably letters. Consider, for example, that the Coptic manuscript contains 500 occurrences of Greek loan-words and that those words contain 2400 letters. Furthermore, the main body of text (without the Prologue) contains 16800 letters - a number not only again divisible by 100, but of enormous symbolic significance (see my website). Is it possible that these three independent numbers just all happen to be divisible by 100? Yes. Given how combinatorial probability works, there's a one in a million chance that that is so. It doesn't take a logician like myself to tell you that that miniscule possibility means nothing against such overwhelming likelihood. The counts, therefore, must have been deliberate, and painstakingly arrived at and maintained. Furthermore, a letter-count divisible by a power of 10 appears to have been one of the marks of "perfection" when one was trying to transform an imperfect piece of text into a perfect one.
There's one other thing I should touch on here, namely the existence of intra-textual meaning. It coexists beside extra-textual meaning, although in some cases the latter is flimsy indeed. Take for example, "If you become my disciples and listen to my words, these stones will be ministers to you" (Th19.2). What is the extra-textual meaning of "these stones"? Are we supposed to envision an historical occasion when Jesus pointed at some actual physical stones? That's pretty thin, but consider the likely intra-textual meaning, namely that the "stones" in question are the sayings themselves. So yes, the textual Jesus is here being made to refer to some "stones" (of a metaphoric kind) which are actually right there in the text! In a later note, I'll explain how the prologue was likely considered to be a "stone" which the "builders" (i.e., puzzle-solvers) were directed to move, but which would constitute the "capstone".
