1. Anokata = Elena Miyano (Shiho/Ai's mom)
This sounds crazy, I know, but I'm 90% sure right now that Anokata is Elena, or at least someone related to her. Remember that her nickname is "Hell Angel" (File 424 p. 12) - this reminds me of what the lady said on the phone to Itakura: "We can be both of God and the devil. Since we are trying to raise the dead against the stream of time" (File 380 p.13). The B.O. is both God and the devil - and Elena is called Hell Angel. Also remember that the lady who said this line has a cat with her (File 398 p.5) - therefore, the lady can't be Vermouth, since she was disguising as Araide during this time, and Araide doesn't have cats (Files 234-237). If it's not Vermouth, it must be another lady who is fluent in English and Japanese - and that includes Elena, who is British and is fluent in Japanese.
Also, Elena's tapes for Haibara are strange. They are numbered #1-20, and each one seems to correspond to Haibara's birthday, since Conan listened to the #11-15 tape and it had Elena talk to 11-year-old Haibara at the beginning (File 425 p. 17). If Elena prepared these tapes right before she was about to be killed by the B.O., why would she prepare so many, instead of just one? And why should she prepare a tape for each of her daughter's birthday in such a short amount of time? My guess is that Elena prepared these tapes each year after her daughter was born, and continued to record the tapes until Shiho disappeared and became Ai - which may mean that Elena is still alive. Also, Haibara hears something strange from the end of the tape that talks to 18-year-old Haibara (File 427 p.9):
In addition, remember that Pisco has served Anokata for a long time - and remember that he was also long-time friends with the Miyano's (File 242 p.9). So who did Pisco serve? Pisco could have served the Miyano's, specifically, Elena. Also remember that Gosho says that he knows what he wants to do with the ending, and that he almost always give the readers enough clues to figure out the mysteries for themselves.
So why do I think that Elena is Anokata and not Atsushi? Because of the discrepancy in the way Akemi and Shiho were treated. Shiho seems to have studied abroad as soon as she was born, while Akemi remained in Japan and lead an almost normal life; Shiho is near the very top of the B.O., while Akemi is near the very bottom; and Shiho and Akemi look nothing alike. Why is there such a discrepancy? My guess is that this is because Shiho and Akemi are actually half-sisters; Akemi must be Atushi's previous wife's, while Shiho is Elena's. This may be why Elena leaves Akemi almost alone while Shiho gets all the special treatment.
I'm not 100% sure about this, but all the evidence seems to point that Elena is Anokata, or at least related to him/her somehow, at least to me. Still, I don't think that she's a bad person, based on the fact that Vermouth doesn't seem entirely like a bad person. I have some ideas about why Elena wants Sherry dead, but they are pure speculation and I can't pull any evidence from the series.
2. Bourbon = Okiya
This is another crazy one, I know - and unlike my previous theory, I'm only about 80% sure about it. I thought that Bourbon = Scar!Akai and Okiya = Akai for the longest time, but I thought that it was too easy - the plot is almost identical to Jodie not being Vermouth and Eisuke not being Kir. I don't think that Gosho would use such a plot for the third time.
The major reason why I don't think that Okiya is Akai is from these scenes, from File 419:
I think that you know where I'm going with this - I think that Akai somehow converted Bourbon (who is most likely the glasses guy who is most likely Okiya) and the hat lady during his stay in the B.O., and those two are continuing to work for Akai.
Also, if Akai is Okiya, why would Okiya say that his favorite color is black because it hides facts about himself while he hates it for the same reason (File 623 p.7)? Why would Akai, who we know is a good person, want to hide anything about himself? It would make sense if Okiya is Bourbon and Akai converted Bourbon - that way, it would be no surprise if Okiya wants to hide facts about himself.
Okiya/Bourbon is also most likely the one who protected Scar!Akai from being shot by Chianti. Gin does not order Chianti to shoot, not because he doesn't think that Scar!Akai is Akai - when he sees Scar!Akai, he thinks, "Akai Shuuichi" (File 704 p.10) - but because Vermouth tells him to, with permission of Anokata (File 704 p.11). After this, Gin complains about the "bastard" "doing as he pleases" (File 704 p.13), and then mentions how he wishes that detectives like Sherlock Holmes would stay fictional (File 704 p.14) - therefore, stopping the shooting most likely has something to do with Bourbon, since Bourbon, like Vermouth, is "secretive" (File 703 p.3) and therefore "does as he pleases," and since Gin mentions Sherlock Holmes, which means that he can't mean Vermouth but Bourbon instead. Therefore, Bourbon must have known about the plan to shoot Scar!Akai - and we know that Okiya was in the department store, and he saw Gin and Chianti (File 703 p.4) and Scar!Akai (File 702 p.16), and therefore knew about the planned shooting. Bourbon/Okiya isn't the only one who attempted to save Scar!Akai - Conan did as well, and why would he do this if Scar!Akai is Bourbon? Also, Okiya criticizes Conan on how he tried to save Scar!Akai, saying that the customers' criticism will be even higher now (File 704 p.15), and it makes no sense for Okiya to criticize Conan unless Okiya tried to save Scar!Akai himself.
So why does Conan recognize Okiya's address? Remember that Conan had Takagi stall glasses guy and hat lady by having him inspect if they were drunk driving or not (File 419 p.18 - the translation here is bad but I checked the original Japanese and that's what it says - yes I know Japanese, I lived in Japan for eight years), so Conan could have known Okiya's address from asking Takagi about the drivers. And this may also be why he trusted Okiya from the beginning, since he thought that Okiya is the FBI who trailed Haibara, though now he seems to realize that he is wrong, based on how he reacted in File 704 p.16.
Therefore, Okiya must be Bourbon, and though I have some doubts, Scar!Akai must be Akai, although it makes no sense to me why Akai would show his plain face in public and risk Rena's life, cutting off potential information he could gain from the CIA.
Ha ha, that turned out way too long. Can you tell that I've been dying to share my theories? X3
EDIT: Man I messed up the links - they should be fixed, now.