I think there are four distinct timelines, yet only snippets of each make up the "true" timeline. To elaborate ...
There is no Flash in this timeline. Barry is born. His mom doesn't die. Time passes. Now we get to Thawne's birth and consequent marriage (this is in the future). We can only assume that somehow Barry (or his descendant) is responsible for the death of Thawne's wife. Once his wife dies, he travels back in time to kill Barry to prevent his her death from occurring (it's assumed he somehow gains his powers in his attempt to unravel the means to travel through time).
Thawne kills Barry's mom. The crucial element to note here is that there is only ONE speedster during Nora's death scene: Thawne. There is no Barry because Barry hasn't been exposed to the particle accelerator yet. From this point forward, this timeline becomes the bulk of what we've been watching; Barry is struck by lightning, becomes the Flash, etc. This continues up until the present episode, when "Out of Time", when ...
...the time jump occurs; Barry goes back in time, essentially undoing most of the events of this episode. He fixes Cisco's death, the Weather Wizard's destruction, and Iris's discovery that Barry is the Flash. Now, things get a little murky and we can only proceed purely by speculation. I'm guessing the events leading up to the death of Thawne's wife are more or less the same, aka Barry is somehow (in)directly responsible. Thus, this time, both Barry and Thawne travel back in time; Thawne to kill young Barry, and (adult) Barry to prevent his mother from dying. Thus...
Timeline 4: (The final one)
THIS is Nora's death as we are shown it; two speedsters racing around her in a ball of lightning. It is at this point that Flash and Reverse Flash travel into the future (for reasons that the future episodes will reveal). This will be our finale and also where Barry disappears.
Looking at time as a continuous "stream":
The order of events is...
Timeline 4: 2 speedsters, Nora Allen dies
Timeline 2: Thawne builds particle accelerator, Barry becomes Flash
Timeline 3: Deus-ex machinima of "Out of Time" (the re-do version)
Timeline 1/3: Events leading up to the death of Thawne's wife
Timeline 4: (future) Grand finale. Battle between Thawn and Barry. Barry's disappearance as noted by the newspaper.