So many questions and so few answers...For those who aren't sure why the "Believe in Kaguya" choice is unavailable on your playthrough, it's because to open that choice you need to finish the Tsubaki route first.
I've seen multiple version/patch references here, not sure outside of the mentioned fix for a Win7 issue what all they do.
If you haven't gotten 100% on the CG/scene. I couldn't tell you why either. I've played through about 7 times and can't get the last Kaguya extra scene to unlock which should unlock her last two CG's. My guess is there's something that has to trigger it, but despite trying to do different things with the few choices I'm given, I don't know what that trigger is. I'm hoping it's as simple as an update. I did try using the "Full save" that was posted on page 3, but that didn't change my available CG's or scenes, so if it does carry something, then my guess is it's in some kind of update that either isn't linked here explaining what it is and isn't part of the OP.
As far as the game goes, it's fairly well written and covers most of the "that makes no sense" statements. Yes there is a system in place for replacing damaged/dead birds to keep up network integrity(must be nice having grand fantasy tech like that). That also makes it kind of impossible to cull their number by sending rednecks after them. As for the removal of existing hardwire networks, I agree, that that would take way too much time, money, and energy to remove, even given the time difference. The better way to look at it would be that without a need, the end-point facilities were probably shut down and the buildings, servers, etc. were repurposed for other uses. Considering the time and money spent setting them up in the first place, it may have been a nigh impossible undertaking to set them up again without the ability to properly organize and communicate given the massive loss of capability given the world's reliance on the pigeon infrastructure that ultimately betrayed them. highly possible that such things were in the works, although the game does point out the massive distrust of technology in general following start of the wave eating.