A longer post will follow with more of my hunt experiences, but first, before I forget it all, I want to share a minor *cough* frustration I encountered.
So the actual answer to the puzzle is here:
http://ihavetofindpeach.com/puzzles/mega_man/recombination/answer/ I got handed this puzzle in, it turns out, a completely solved state. That is, they had done exactly what they were supposed to do except that they only did it once. They even got "ALLINCLAPC", which was described as "ALLIN followed by garbage, like the other clues". Note that you are doing exactly the same thing you did before, when each clue came with a bunch of garbage letters at the end that you ignore, and it very specifically has an end point that does not connect with something to form a complete cycle. I have no idea how the C migrates to the front of that clue. All in all, I have no idea why we were supposed to prefer "ALLINCLAPC" to "ALLIN" which followed the pattern established up to that point, but I wasn't involved in any of this so there might well be a good reason.
I just got handed an already-solved puzzle and told that this answer wasn't the answer, the obvious extraction mechanism wasn't the extraction mechanism and here are 5 numbers, 5 words and a bunch of unused information.
First, there was the title. It could refer to taking letters from multiple words and combining them into one word, but that is what we do in very nearly every puzzle. It's sort of like getting a college titled "Black And White" and having it refer to the color of letters on the paper. However, "recombination" and "juggling" are two of three terms for non-destructive genetic mutation, along with "reshuffling". So to me, this puzzle was clearly cluing DNA. Up, down and sideways. Not only that, but my five words all have A,T,C,G.
This is when I went off into apparent lala land.
First, I got one set of [A,C,T,G] by indexing into the words with the number of the puzzle where they are juggled, with the fourth word producing "R", which I couldn't decide if it was a clue that this was RNA (you'll see), or just ignored. That makes sense. Then I have all these extra, repetitive, unused letters at the end of each letter. If I counted them I, and an independent counters, got consistent-but-different-from-reported-in-the-answer numbers, in the same range of 3 to 7 as the original numbers (though non-unique this time), which give another set of [A,C,T,G], with one clue producing no letter at all. I liked the dual strand idea and that I had some concrete connections.
So now I have two sets of four words in pairs. Three words were tied to two other words, two words were tied to only one other word. It did not give an ordering, except that CATNIP had ended the cycle earlier, so I stuck it on the bottom while not being completely satisfied with that if it came up later.
Now this digression down lala land would probably have been abandoned and we'd eventually have backsolved it, except that this is what you get when you put these together in the given configuration:
...OCARINA
ILLOGIC
....CONCEIT
........GRAIL
........CATNIP
One diagonal. A 5-nucleotide sequence: ACCGA, which uses letters not used while putting this together (not necessary, but still aesthetically pleasing.) This appeared absolutely clear, unique and well-clued in my brain at that point in the hunt (it even kind of looks like half a double-helix.)
It's not clear if it is RNA or DNA, but since I had transcribed the sequences according to the DNA, which is how RNA is usually produced, I figured RNA was the stronger position (plus, the extra R might be cluing, who knows) . It you extract every possible amino acid in that sequence (ACC, CCG, CGA), you get TPR, which is a human gene that causes thyroid cancer when it experiences recombination errors. However, there is no indication of where to go from there (of course, since I was never supposed to get here in the first place.) I had no indication of Latin vs. English name, for example. I called in thyroid cancer, just in case it was simple and poorly constrained.
I really kind of wanted to anagram, since then I'd have juggling, recombination and reshuffling. THYROID CANCER wasn't going to help, and neither were the three-letter versions of those amino acids. So I produced four sets of three letters by extracting forwards, then backwards, then the transcribed sequence (that is, as though this were DNA instead of the RNA I had assumed it was) backwards and forwards. I liked this even more because it meant it didn't matter that it didn't clue up-from-down or RNA-from-DNA strongly; those orientations just didn't matter! I took the three-letter abbreviations of their amino acids and then discarded (I think it was, don't quite remember) all the adjacent-and-stacked letters. Which makes sense, because in recombination errors only the changes matter; if you swap an A for an A it is irrelevant. From these poor, over-worked five letters I had wrestled free a set of seven letters that anagram into ORAL STREP.
Finally! Success! The only unused information one discarded R instead of almost half the information in the puzzle! Recombination, juggling and reshuffling! It even fit the pattern we'd seen in the meta (everything up to that point (that is to say, two puzzles) had been a two-word disease or plague of some kind; ORAL STREP sounded unpleasant to me and was two words, if a little short.)
When I called this answer in, though, in the guy on the phone said, "you really should try solving this forward; it is a good puzzle." Clearly he saw that we'd almost had it, time passed and then I'd called in THYROID CANCER and figured that I was now randomly choosing two-word disease phrases as awkward as "ORAL STREP"? Whatever his reasoning, however well-intentioned his "stop guessing" chiding was, it felt like a punch in the gut.
I had just spent about 45 minutes following a train of logic that if it weren't so clearly correct as I went along, and elegant and rewarding, would have been frustrating all on its own. Then I had spent at least another hour and a half, probably more, attempting to wring an answer from it before hitting on the backwards&forwards idea. I thought that, after two hours post-work-doing, when the obvious answer was reported to be wrong I was no longer obliged to think it was a good puzzle. In fact, he appeared to think that instead of devoting hours to his his "good" puzzle, I might as well be backsolving.
So I went out and cried my frustration off in the hall and then unproductively obsessed for a while, and went to sleep and woke up and obsessed for a while longer until I finally gave up in a depressed, frustrated huff. When the answers went up I immediately went to look, hoping to discover that I was just too stupid to figure out the obvious and elegant thing I should have done instead. Instead, it was the most unsatisfying conclusion to a puzzle story thus far: it was already solved, but the clue phrase looked like garbage, so I invented an entire puzzle on top of it. Well, I think my version of the puzzle was good-er than that clue phrase, so there condescending Mr. You-Might-As-Well-Be-Guessing-Randomly-As-Trying-To-Solve-This-Puzzle.
So, in conclusion, the theme of this hunt for me was pretty much "you might as well be backsolving." And don't get cancer *or* oral strep, because neither of them is the answer, apparently.