I don't think that every time we have seen River she is younger. She got the Vortex Manipulator during the Pandorica (then gives it to the doctor and gets it back at the very end of Big Bang), and she has it during the episodes with the Silence. She also is wearing the same outfit at the end of Demon's Run as she was at the end of the Season opener with the Silence - complete with Vortex Manipulator.
Also, note that she never says that from her perspective Pandorica and Byzantium were adjacent - just that she "Remembers" the Pandorica and she knows that from the Doctor's perspective, it is next (that's Amy's fault because she said so during Pandorica.)
So I'm figuring that from River's perspective we have at least the following:
- Pandorica Opens and Big Bang
- Silence and the end of "A Good Man Goes to War"
- Crash of Byzantium
- The Singing Towers (off screen - she said it's the last time she saw Dr.)
- The Library
But where I'm still puzzling is -
the beginning to "A Good Man Goes to War" - she seems to remember Demon's Run, and her relationship with the Doctor seems close. She also seems to be surprised to see Rory (maybe she has been with a future version of the doctor who doesn't have Rory around?)
But to puzzle it out.... let's say Silence happened when Amy was about 2 - 3 months pregnant. Doctor drops off River. River heads to Demon's Run the same day. Then she is tasked with seeing Amy and Rory home - something we won't know much about till Fall. During that time, something happens to Rory. She then heads back to the same day that she had left prison (b/c otherwise the guards would be after her.). Meanwhile, Dr. and Rory and Amy have adventures that we have seen. Amy goes into labor. One month later, Dr shows up at Demons Run (mentioned in the show - "it's been a month and he hasn't done anything!"). Rory goes to pick up River - it's been around 7 to 8 months "straight time" since River was at Demon's run - that's why she can't go back - she knows she's already there.
My sense, given that in Crash of Byzantium she is trying to earn her pardon and she seems very aware that she does not have a close relationship with the doctor, that it is much later in her timestream - closer to the Library. And therefore, I would adjust the timeline so:
- Pandorica Opens and Big Bang
- Jim the Fish (off screen - I'm guessing here, because she asked about this, not Pandorica during the Silence episode)
- Silence and the end of "A Good Man Goes to War"
- (off screen stuff)
- Beginning of "A Good Man Goes to War"
- Crash of Byzantium
- The Singing Towers
- The Library
Now, if we assume, as we have been led to, that the young girl is River, we have this:
- Young River in the Silence
- Pandorica Opens and Big Bang
- Jim the Fish
- Silence and the end of "A Good Man Goes to War"
- (off screen stuff)
- Beginning of "A Good Man Goes to War"
- Crash of Byzantium
- The Singing Towers
- The Library
Of course, we don't know if she shoots the doctor or not (good arguments either way - I'm going with she DOES because it makes the "he knew all about me" that much more potent.) - but if we assume she does, we also don't know WHEN. I'm going to wager a guess that it occurs BEFORE she escapes the suit:
- Young River kills the Doctor
- Young River in the Silence
- Pandorica Opens and Big Bang
- Jim the Fish
- Silence and the end of "A Good Man Goes to War"
- (off screen stuff)
- Beginning of "A Good Man Goes to War"
- Crash of Byzantium
- The Singing Towers
- The Library
And just making conjecture - I think the Dr. won't be able to find her until after the events that he is already wrapped up in. So...
- Young River kills the Doctor
- Young River in the Silence
- Doctor locates a young River
- (off screen stuff)
- Pandorica Opens and Big Bang
- Jim the Fish
- Silence and the end of "A Good Man Goes to War"
- (off screen stuff)
- Beginning of "A Good Man Goes to War"
- Crash of Byzantium
- The Singing Towers
- The Library
And one more point.... We DO know that she did not have the Vortex Manipulator during the last part of the Big Bang - the Dr. had it. What we dont' know is how on earth she ended up at Amy's wedding! There's something fishy there - and I have to wonder if it's another out of timestream event. I can't figure it out, so for now, this is the best I can do.
And yes, it is "mostly" backwards, but not totally backwards. Clearly the doctor himself broke that trend by saying goodbye to her at the Singing Towers as a much later version of himself. (We know that because it is a screwdriver we haven't seen yet). So the last time River sees the doctor is probably a very late version of her doctor, making it a very special moment for them both.
EDIT:
I also don't believe she's in prison because she killed someone. I think that's just the line. Remember, she was raised to be a weapon against the doctor. In the Time of Angels, the Bishop says "you're the only one who can control him - that's why you are here - but it only works if he doesn't know who you are."
I think the clerics have her in Stormcage so that they can pull her out to use her against the doctor whenever they feel like it. Either they or the Silence had her kill the doctor, but they know he's a time traveler and could show up again. River is in jail because they want her there. But she STAYS in jail because she promised the doctor she would.
That's my theory anyway... :)