Masumi said she came to Japan to meet the "wizard/magician," and often mentions that word or words like it while around Shinichi/Conan, suggesting he's the "wizard/magician," and that he's the reason she's in Japan. While she, like Shiho/Ai, is in love with Shinichi/Conan, she's not in Japan because of him—it's likely because MG (her mother, in all probability) was shrunk recently. If so, and she says that she came to Japan to meet the "wizard/magician," she can't be referring to Shinichi/Conan. The "wizard/magician" is either referring to MG or Shiho/Ai.
As for the middle brother's text, I don't think his response to her asking how he knew Shinichi/Conan was "I know he's Shinichi," or something like that—her expression, upon seeing such a response, would have been surprise, at first... but all she does is smile, blush, and think, "I see... so that's how it is...". If Shukichi is the middle brother, and had been sheltering MG before she moved in with Masumi at some point before File 856—if MG had been with Masumi since before File 768, you'd think she would've found out about Shinichi/Conan earlier and, thus, wanted to meet with him, earlier—there's no reason to think he'd discount the possibility of someone shrinking, especially if he remembered Shinichi's young face. Maybe the reason he looked so shocked in File 849 at Shinichi/Conan citing what he said in File 848—and, also, figuring out the case, as he had—was because it made the possibility that Conan was a shrunken Shinichi all the more likely. Perhaps the "A well-prepared move... that's what this is..." line slipped out of Shukichi, or he said it to see if Shinichi/Conan could solve the case, as he had—we don't see his reaction to seeing Shinichi/Conan, after all—or maybe it was both. Heck, MG could've been in his suite during that case, for all we know... I think that at some point between Mystery Train (Files 818–824) and Steamy Relations (Files 856–858), MG moved in with Masumi.
We've never seen MG talk to Masumi via phone, so she was likely talking to her middle brother at the end of File 800 (Online Client/Detectives' Nocturne). He could've been giving her an update on MG's condition, since she seems to be in perpetual cold-mode (cold as in sick, not ice, or something like it). Speaking of that case, along with File 777 (Target on Tape), it really seems that she's alone in that apartment—there doesn't really seem to be a place where MG could've been, at the time (you could say bathroom and I'd have to say it can't be proven, either way, though).