The source code is a computer program which creates a worm hole to plug any consciousness into other similar parallel universes it can locate based on its input data. This input data is the data from all the minds on the train (i.e. all the people who died) whose last 8 minutes of existence have been recaptured to locate the exact time, place and event that we want someones consciousness to be plugged into. The source code can theoretically plug any consciousness into an almost identical (parallel) universe to our own. This is exactly what is happening in the movie every time captain Colter Stevens is made to replay those last 8 minutes. Remember also, a single consciousness cannot exist simultaneously in more than one reality/universe and one universe cannot directly affect another. Obviously, the pod thing we see Colter Stevens in is just the projected (by Colter) computer interface used to communicate with the subject in one reality. It could be a hammock on a beach if Colter's consciousness wanted it!
Keeping this in mind, there are essentially only two realities in the movie; since all the realities in which Colter dies are lost, we can ignore those and concentrate on what happens at the end. First, let's explain the death sequence. Since a single consciousness cannot exist in more than one universe and the source code provides a connection between universes, when Colter dies in one reality, his consciousness will revert back to the other, regardless of which reality he dies in. Now, at the end, when Colter sends the email, speaks to his father, and calls Dr Rutledge's office, he is doing this in reality B (the 8 minute playback reality) so events will play out as would be predicted (same as reality A since they are essentially the same in terms of physics) i.e. Rutledge would receive some pizza, Goodwin will receive the email and Colter's father is a happy man. In reality A, the train has already exploded and a second terrorist attack is imminent, as explained in the movie. One can essentially think of reality B as exactly the same as reality A with the only difference being that Sean Fentress's consciousness has been replaced by Colter Stevens. This would explain why Colter still looks like Sean at the end of the movie, why he continues to live (he's in a different universe) and, more importantly, solve the so-called goof of the bomber.
The minds of the dead people are essentially only used to locate the exact time, place and event that we want someone's consciousness to be plugged into. Since it is a parallel universe, those people are real, independent people as in any universe. Therefore the bomber, although he clearly didn't die in reality A (or he couldn't have been caught, preventing the second terrorist attack), he still exists as an independent entity in reality B, therefore no need for his last 8 minutes as his plans, explosives and motives are the same in both universes. It is from the moment Colter evades the explosion that the two universes start to become more different and the timelines of each universe go in their separate directions. Finally, killing Colter in reality A meant his consciousness is now stuck in reality B and he lives a normal life in that parallel universe as Sean Fentress. The Colter Stevens of reality A is being used in the source code project, meaning that soon he will die, too, due to the source code program being turned off and only Colter left is in reality B.
It could be clarified that each particular *instance* of a consciousness can only exist in one reality at at time, but the Source Code device can project a particular instance of a consciousness from one reality to a parallel one--causing multiple instances of that consciousness in the destination parallel universe, as happens in the movie.
At the end of the movie, reality B contains *two* instances of Coulter's consciousness--a new instance of Coulter's consciousness, projected into Fentress' body from parallel universe "reality A" by the Source Code device, and reality B's original instance of Coulter's consciousness, in his ruined body in the Source Code chamber. In reality B, the train bomb never detonates and the dirty nuke is seized before it becomes a threat, so its original instance of Coulter's consciousness, in his body in the Source Code chamber, is never called into action, and remains ready for a sequel.