Seems like our journey was quite different to several people here! Maybe because the puzzle's been tweaked (we were playing version 1.25) or maybe because we're used to Mystery Hunt style puzzles. We spotted the cryptic numbers at the bottom of each puzzle and considered a few interpretations, though we progressed through puzzles 1-3 in the normal way (MOBSTER, RESET etc). We were carefully noting down each letter that was obscured in case those spelled something. It was around puzzle 4 or 5 that we realised what the letters at the bottom mean (it helps that we're veterans of Edrith's Quizzes that use the same notation, and puzzles 4-5 are two of the easiest sequences to spot) - though even there there was some reconsideration of inferred rules because 4 can be solved in "ortho-Boggle" style with no diagonals, but 5 can't. At that point we went back and solved 2-5 in the true way, though we still had no idea what to do with 1 or 6. Around this point we had the idea to start highlighting leftover letters and found the connection to the bottom-right clue as well. From that point 7, 9 and 10 were straightforward (though 10 played some fun tricks with the blobs); we'd realised some of the words are listed reversed, but 9 was I think the clearest confirmation that it's specifically the right-hand words that are mirrored. We'd been expecting a metapuzzle so solved 11 fairly easily, and found 0 didn't really tell us anything new - only confirmed the rules we'd already inferred. Then on about the third or fourth look back at puzzle 1 we finally worked out what 1 was doing (I've only heard of one of the five given kinds of cookie, but thankfully my wife reads American recipes) and knocked that one out. 12 was a very satisfying conclusion, drawing everything together, and so delightful how the final extraction could only by solved by combining three strands of "leftovers of 12", "traceable string in 12" and "English letter patterns". Amusingly, the one thing we missed until the final page was the count of answers - we hadn't noticed that there were exactly twelve words to find in each puzzle, even though we'd found them all!
Thanks so much for making the puzzle, and now we're very much looking forward to trying the sequel :)