I think that Akai is alive, and I think the plan somehow is similar to what happened to when Andre was driving with Hidemi. I believe, first off, Hidemi and Akai (and maybe Conan) had discussed what the Organization might do if she was to join back in (while in the hospital). Somehow, Kir somehow stuck a hidden message into either the text or in her call, or otherwise Akai was already prepared and figured something like this would happen. He went to Reiha pass and investigated. He probably did notice the Organization a long distance away, so he purposely pulled his truck over by the ledge of the cliff, just like how Andre pulled his truck over to the side. He prepared fake blood beforehand on the spots he would be sure Kir would shoot or stab, weak points in the body like the head, heart, and lungs (maybe even the throat).He also put one in his mouth to make it seem he was letting out blood through there too. Kir shot him twice, and he fell into the car. She set off the bomb with 3 seconds (30 seconds in the manga), to which I believe Akai escaped out of the car while she was turned, since the Organization was watching him via the camera on her choker. As for the dead body, I believe it was Rikumichi's dead body. We do not know what happened to him after his death, only that the FBI tried to keep this a secret from the Organization. If the police were to do a search, they would see a bullet wound to the head, where both Akai and Rikumichi were shot. The fingerprints can be explained because earlier on, Rikumichi touched Conan's phone. Plus, I find it strange the gun was shot at Akai, but he looked perfectly fine until a moment later, when he started bleeding and crouched down.I also find it strange Akai came with no weapon at all, and took the shot to the lungs and head so easily, and even made his last words sound funny. "To think you've gone this far..." with a smile on his face... plus the fact his hand stayed in his pocket the entire time seemed peculiar... also the fact when Kir turned away for a moment, then looked back, they didn't show the eyes of the person in the car, but the head was turned differently than before... at first, the head was facing to the left, but after she turned away, the head was facing forward, and we didn't get a glimpse of the eyes on the body. I'm not saying that Akai got out of his clothes and put them on the body at that moment, but maybe he had the body prepared with his clothes and his cell phone, which he couldn't use if he was pretending to be dead... he didn't tell anyone because he wanted their reactions to be realistic, plus he may not want any information to get leaked to the Black Organization... he disguised as Okiya Subaru by using a wig, changing his outfit, and wearing high powered glasses to make it hard to see and forcing him to squint, then assumed the role of a college student. He moved into Shinichi's house because Conan knew his plan probably, or saw through his disguise, and gives Haibara that feeling not because he's Bourbon but because he was once the BO member Rye. Him drinking Bourbon does not prove he is Bourbon, since Bourbon is Akai's favorite drink. Plus Akai and Okiya compare the BO to wolves.
Bourbon on the other hand disguised as Akai because he got suspicious Akai was alive. He did this so he could gain more information by viewing reactions of FBI agents, and was trying to lure out Akai. Akai, as Okiya, decided to visit the bank Bourbon had been at during the robbery case, and may have noticed him entering the mall. He followed him to see what he was doing, then left a note for Jodie saying to leave because there was danger. This may have not been because of the bomber, but because he was warning her about Scar Akai, or Bourbon.