I love this story, but I believe your Beta-team are correct. It seems to me that you have grown so fond of using small, tiny pointers, and plot-forwarders (in lack of words), that you have missed something rather essential:
You put them in, because to YOU, they are intriguing and small, seemingly forgetting that YOU know the plot and will spot them emmediately yourself. See, we readers do not know the plot, unless we get those pointers. Myself, I LOVE small pointers and intelligent fics, but I still want the bigger ones every once in a while, so that the plot has an obvious feeling of moving forward... Not only that - imagine what you could hide, if you gave us several plot-parts at once, creating overload of info, and then hid the miniscule, but ever-so-important ones among those?
I also think it's time to move forward in the story... you're not even at the end of September, apparently, while the readers (at least mine and my fiance's) internal clocks say it should be Halloween or Christmas soon. There's no shame in time-jumping.
My regards to your Beta-team aswell. Consider yourself lucky, you seem to have a good circle around you. This is usually very hard to achieve!
Cheers, and well done!