Will Amuro get killed for knowing too much? Defect? Discover Akai and force Kir out of the organization?
I can't see Kir losing her place within the BO, because up to this point her intel was (as far as we know) pretty much non-existent. The only information we saw her give to the FBI is that Bourbon entered the game, which was by itself a big deal, but I think it would somehow feel wrong if that was all she could discover. Furthermore: if she would be forced out she would be forced out in a lethal manner and her role is not played out (IMO at least).
On the other hand since they are obviously not sure that Akai is dead, she probably isn't getting any information at the moment.
And this just crossed my mind: Bourbon might have been a leak intended by the BO.
Considering this Amuro either won't discover Akai, which at this point in Amuros investigations will require an extraordinary maneuver by Conan and Akai, or he won't disclose the information about Akai by choice or the lack of opportunity to do so due to not being alive.
I can't really see him opting for defection, because his hate of Akai is rather well established, although as far as I know the reason for hating him is still subject to speculation.
And there don't come any reasons for defection to mind... he doesn't have any relations (yet) with one on Conan's side that would justify a defection (unless you buy into the Amuro-is-the-second-brother-theory)
Well... there is the promise he made to Vermouth, but we have no clue whatsoever what it entailed and I can't see him agreeing to terms that would put Vermouth over the BO
My reasoning leaves me only with him getting killed, which is a problematic assumption itself due to the lack of possible killers. Personally I only see five people and for each of them a strong counter argument can be made...
Kir – I believe she is willing to kill to assure her place as a NOC in the BO, but actually killing him would endanger exactly this position...
Akai – we don't actually know how his moral compass works, but of all the FBI agents we have seen so far, I consider him the only one going down that road; however this has not been established and he would endanger his disguise by doing so... hence, unlikely
Vermouth – she obviously is determined to not let anybody know about the side effects of APTX (as seen in the Bell Tree Express) and Bourbon seems close to figuring out Conan's (and by extension Haibara's) secret; there we have a motive and a ruthless perpetrator, but killing another BO-agent would change the dynamics drastically (which I personally would welcome) and is problematic for obvious reasons
Haibara – I guess many who will read this will think that at this point I have lost it, but to me someone who is willing to sacrifice herself to save her friends, would also kill to achieve the same goal (if there are no other options available); of course she has changed since she worked for the BO and I guess even then she wasn't entirely comfortable with killing (although I guess she prefered it over dying) and she is strongly influenced by the no-kill Kudo, but for me the only real reason that won't happen is that given her condition and circumstances she won't ever get the chance to kill Bourbon
Gin – only one I can come up with who can kill Bourbon without endangering the status quo; but how we get from where we are to Gin having a reason to kill Bourbon (without the aforementioned unlikely defection) is beyond me
Thinking about how many reasons there are against all these scenarios, made me really excited about the resolution!
How will Conan force Amuro out before he knows too much? Will he have to trick him, desperate revival style?
I get the feeling Amuro already knows (or at least suspects) too much... but then again I probably assume too much on this front, since I tend to fill in the blanks, Gosho intentionally leaves, with knowledge of my own (I hope I am not the only one doing that).
The blanks that struck me:
We didn't get to see Vermouth's reaction to Bourbon refering to Conan as a 'terrifying man'... for me that is the most interesting one since Vermouth can't be too happy that Bourbon is doubting Conan's youthful exterior
We didn't see when Amuro started listening to Conan calling Haibara and we didn't see whether or not Conan adressed her at any point by her name... nevertheless: assuming he heard the comment about 'the certain smell' (otherwise it would be pointless to have him there because after that there is no valuable information to be gained on Conan's end of the conversation), the only conclusion (IMO) to be drawn there is that Conan called either Akai or Sherry... [counter arguments welcome!]
What will happen if someone brings up Shinichi being alive in front of Amuro?
Let's change this to...
WHEN someone brings up Shinichi being alive in front of Amuro... I mean the number of imbeciles around who only wait to slip up on that account is way to high that this wouldn't happen.
Ran (and Sonoko) – who weren't able to conceal Shinichi's identity from Okiya despite being explicitely asked
Heiji – who barges into the detective agency calling 'Kudo' without first checking who is present; i doubt Amuro would fall for the 'kudoi'-bit he puts on every now and then
Kazuha – who has nothing better to discuss with Ran as her relationship with Kudo
Sera – who was complicit in telling Okiya, although I think she is the most reasonable in that regard
Agasa and Haibara – who never came around to calling Conan by his fake name despite being bugged on numerous occasions and who will most likely be bugged again really soon
To sum it up: just a matter of time!
Assuming that it will take Amuro about half a day to reach the inevitable conclusion that Conan=Kudo, I seriously hope Conan has come up with a contingency plan for that scenario, but I doubt it will be desperate revival style, since that would inform the BO that Shinichi is in fact alive, putting everyone in danger Conan cares about.
We can only hope, that the promise Bourbon made to Vermouth actually prevents him from sharing this intel. I say hope, because I highly doubt it!
Will Sera's second brother be good or evil? What has he been doing? Who is he and how does he know Conan?
At this point in the story evil is probably a synonym for being in the BO and that I doubt... more a gut feeling than anything else.
The who-question is the most compelling one and when this is answered his past and relation to Conan will fall right into place.
And I think this question deserves its own thread.
Questions, Chekhov might have forgotten:
Will Jodie and the FBI figure out, that Akai is still alive? If yes, will they do so before Bourbon? If yes, will they be capable of keeping it a secret?
(I personally liked that Jodie was actually onto something in her last appearance, connecting dots. I mean, she has gotten pretty incapable of late and despite not being back to her former self – all this babbling about undercover investigations and operations in front of a civilian, as far as she was concerned, made me cringe- it was a step in the right direction. She was one of my favourites in the Vermouth-arc and it went steeply downhill from there.)
Will Sera discover Akai?
Will Ran figure out, that Conan is Shinichi? (Probably not, but a suspicion arc is coming.)
And by the way... you showered us with questions, Chekhov, but didn't grace us with your predictions! Are you waiting for a certain number of people to share their ideas, hopes and dreams

, before you give us insight in Gosho's notebook?