I've had a fab time with this, and so has my son (14) for whom I printed a separate copy. He assiduously followed the instructions and highlighted only the given words until the proper time; I spotted what was going on in #4 and completed it, then was on the lookout (but couldn't do them all until #0). On the other hand, he noticed the reason for the doodle on page 10 and had to tell me, and he quickly got what the codes at the bottom were (which I didn't twig to at all, despite it being really obvious in retrospect, especially on #11! Which made #1 a lot harder).
I am in favour of the with-zero version, which we used: the confirmation of the suspected rules is very helpful.
(But on that note, perhaps a bug? v1.17 had a total of 150 for the with-zero version but v1.19 landscape (ie with zero) has a total of 144.)
I like the new checkbox at the end; I do think it's a good idea to let the user know they've seen "the ending". I do The Listener cryptic crossword, and there's often an endgame that involves highlighting something or writing something below the grid, to wrap everything up nicely, and it's very satisfying. Would there be any value in having the checkbox text be (eg, apologies for how hackneyed it sounds) "The word searches are done / _______" and a box or line intended for the player to write the final message on. That idea could be terrible, ignore it at will and you're obviously a better designer; the idea is that more than a score or checkbox, the player is asked to enter the final thing that it's all been building up to, and the context (and the cheap rhyme) confirms that it's the right thing to have written.
My own journey at the end involved not noticing the meanings of the even-numbered leftovers and thinking it was all a bit random, until I revisited it and read #4's item in the grid "incorrectly". Fortunately that quickly got me to the end.
Anyway, loved it, great work and well done on finding so many fun things to do around the word search concept. I've been spreading the word among my peers. Oh, and I came here from the Thinky Awards too.
Cheers,
Steve