Your theory doesn't make much sense motive-wise or why-characters-do-certain-things-wise, which you did point out several times. Conan's behavior regarding Okiya is also questionable as well. Finally there are the usual contradictions regarding Okiya being Bourbon which I will get to later.
What's the purpose, who is the target, and whose side is Amuro on? Why appear in front of the FBI when a single agent is alone? As you noted, Okiya's motive for calling off scar Akai's assassination isn't clear. Except the order came from Bourbon through Vermouth. Why would Vermouth use the boss's name for this? Why text Kogoro and not Conan if there was a message for him? If Scar Akai knows Conan is behind Kogoro, he would know that Conan could solve the case on his own without his help, or at the very least could text Conan and would know Conan would use it when doing sleeping Kogoro. This of course begs the question of how Scar Akai would know Kogoro's phone number, or would know Conan beyond what he saw at Teito bank.Also, Conan didn't know who sent the message at first. (704p2) It was only through Ran's intervention that Conan found out who sent the message in the first place because Conan didn't think Ran's technique would work. (704p4) Scar Akai couldn't have counted on Ran. Also what part of the quoted stuff sounds like it has double meaning beyond what it meant to the case? Scar Akai wasn't waving flags around, and he did want to leave.
Only if Sera knows Tohru. I don't think they have met, but their reaction in the next file should cement this.Finally, we have the usual contradictions to Okiya being Bourbon.
How does Okiya know about the tracking glasses and badges? Conan has never used the tracking glasses in front of Okiya, and the operating mechanism isn't obvious.
Why does Conan trust Okiya to lend him his house, and tell him about Shinichi in the process? Once in Shinichi's house, Okiya will and does find out for sure that Shinichi is alive and perhaps that Conan is Shinichi. The "put him there to watch him" strategy is far too dangerous for Conan to try, which Conan acknowledges when Haibara suggests it. Conan's strategy would also mean he violated his one guiding principle to keep Ran away from the Black Org, because Ran will definitely run into Okiya if Conan keeps him in his house.
Why does Conan let Okiya anywhere near Haibara? Haibara is obviously Shiho, so if Bourbon is loyal, that should be a death warrant for Shiho, Agasa, and Conan at the least, yet they are still alive after a long time, and Okiya has had plenty of opportunities to kill them, which he can ascertain using the listening devices he planted there.
Why did Conan know about/react to Okiya's address before meeting him if Conan only found out about Bourbon that very day?
Why does Ran feel like Okiya is familiar somehow if Okiya is Bourbon and they haven't met before?
What about the Gundam Char Aznable naming scheme?