For the poll, too bad we can't double-vote. I selected that Subaru Okiya is Bourbon because that's the main question, but I also think that Tooru Amuro is indeed Scar Akai (to me, the whole thing is that Scar Akai isn't in fact Bourbon despite what we are naturally led to believe).
My line of reasoning is the following:
Tooru Amuro and Subaru Okiya both knew Shuichi Akai. Subaru is Bourbon.
Tooru Amuro is Scar Akai but, for some reason, his disguise is meant in such a way that it would be obvious for someone with detective abilities and who knew Shuichi Akai that he isn't the real deal (right-handed, burnt on the wrong side for those who saw the murder...).
Seeing Shuichi Akai appearing, Subaru comes to investigate. To see him closely allows him to deduce Scar Akai's true identity (Tooru Amuro). Spotting the BO agents on the streets, he contacts the boss and Vermouth to tell Gin (with whom he doesn't get along) to let Scar Akai leave for some reason. Gin wouldn't like Bourbon's methods and he would be pissed off, but he would obey an order coming directly from the boss.
As for Conan, I think Scar Akai has left him some kind of message with the text message to Kogoro.
"Flag signaling is used when it's difficult to convey verbal messages."
"The above are my deductions. Hurry and complete your investigation so that we may be released."
I wonder if this message was really only meant for Kogoro or if Scar Akai tried to make contact with Conan without revealing himself directly. Of course, he would know him somehow, given the fact that he also saved his life by the past.
As for Masumi Sera, I think that she is indeed searching for her missing brother and that she thinks Tooru has some informations on his whereabouts.