In regards to Haibara still not being able to make a permanent antidote to APTX, in my opinion even if she did manage to create it, it won't really be all that useful. Shinichi got lucky when he survived the poison because he could take on the identity of Conan and hide himself from the BO. If he took the antidote now he would just be targeted. So maybe it's possible Haibara has almost finished the cure but sees no reason to tell Conan yet.
Regarding Shinichi not telling Ran the truth, this most likely just has to do with the whole concept of the storyline. While it may be true that by not telling her the truth that Shinichi is protecting Ran, it's really not all that serious since like 6+ other people already know his identity. The main reasons she can't find out is because the story would just be boring/awkward (imagine a case where Conan doesn't have to pretend to be a child to fool Ran anymore and so he can just solve the case himself without using Mouri). Also Shinichi said a couple times already that he "won't tell Ran how he feels untill he gets his original body back", and I believe he'll do just that.
Also I think I noticed a bit of a plothole. When Kaitou Kid was first introduced to the series Conan had never heard of him before. Yet in one of the specials they showed a little duel between Shinichi (before he was turned into Conan) and Kid, are we supposed to believe he forgot about that ? (Although this is just from the anime, if this isn't canon then I guess it would make sense).