We could likely make an educated guess as to the order of events, based on when Shaw is in her underwear vs when she is in the space-suit. There are alot of other clues also. This is the rough order I think events might occur in (I seperated a few events that I can't seem to blend together):
Spoiler
Humans land at site and start to investigate.
Vickers is in a light-blue, collared outfit at this time(as well as earlier during the ancient star-chart comparisions).
Shaw(suit) is investigating site after landing.
Shaw(suit) has a tear looking up at something she sees(mural?).
David is facinated by animated alien-goo seen at the mound-site.
Mohawk guy(pre-infection) comments on the slime moving.
The human site-investigation turns nasty: "I got a ping" "Are these things moving?" "This thing has opened up from the inside" "It's in my throat. It's in my throat!"
Someone(David?) takes a container of Alien-goo back to Prometheus.
Shaw(naked? underwear?) in bed with Charlie(possibly how she gets infected). Charlie's head in his own hands(stressed?).
Charlie notices he is infected. He may have known before bed-scene.
Shaw(clothing?) sees someone else infected(in window, with tentacle). Her lover Charlie, now fully infected? There is also another woman that is likely infected, who wakes up and bashes the anti-infection-suit guy with a bar of some type(IMAX trailer).
Shaw(underwear) clasps her hands together suddenly with the thought of something bad(she knows she is infected? Knows earth is going to die? She has to kill the infected crew-member(Charlie?) on other side of door/window?). "Cut it off! Cut it off!" is being said at this moment(US trailer), so she is likely seeing an infected crew-member.
Shaw(underwear) is infected/pregnant.
Shaw(underwear) is operated on.
Shaw(underwear) is in hallway, limping along.
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Vickers is in black skin-suit when Derelict is first seen by humans. "What is that?" "It is a ship"
Shaw(in suit) on planet surface, leaping across opening launch doors, pleading that there might not be any earth to go back to. Is this scene pre-infection? If so, why do we see her infected in underwear in human hallways/rooms?
Motionless Vickers(black skin-suit) in hallway, seeing something(SJ? Infected person?).
Vickers(black skin-suit) running through hallway, likely headed to escape-pod.
Escape-pod looking item ejecting from Prometheus, apparently before Prometheus hits the Derelict.
Captain is making an O-face(likely crashing Prometheus into the Derilict intentionally).
Shaw(in suit) escapes crashing Derelict.
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"Kill everything". It is safe to say that this occurs after the infection breaks out, before the fight with mutant happens.
Infected Mohawk guy fights in Prometheus bay.
Space Jockey(s) awake.
A SJ confronts a male & scared female crew member in a room.
Shaw(in suit) is on her butt, up against wall, with SJ in front of her.
Shaw(in suit) has axe in her hand(likely fighting a SJ?).
Comment: To me, it seems like there are human conversations and activity in human-rooms that take place after the Derelict is rammed by Prometheus. Shaw: "We were so wrong" seems to take place in a human-room after a major event(crashed Derelict? Infection breaks out?). Or... does the infection break out, Shaw is operated on, she then says "We were so wrong", and THEN the Space Jockeys wake up and start to depart to Earth when Shaw is back in her suit and investigating planet again(with SJ launch-doors opening)? Also, the scene where Shaw is limping through hallway in underwear, with staples, there are suits in background, but the mobile vehicle is not big enough represent that hallway, so that limping scene must still be on Prometheus before the crash/ramming. When Shaw has axe in her hand(IMAX trailer), there is debris in hallway behind her, so maybe she is inside the Prometheus wreckage(but with functioning hallway light-panels?).
Unanswered questions:
When is Vickers naked? She tears her black skin-suit a bit around neck, as she is running. But gets in escape-pod clothed.
Is the dust-storm natural weather(unlikely), caused by the Derelict ship taking off(possibility due to Derelict departure being seen when humans are still investigating site), caused by the crashed Derelict (slightly unlikely since we see humans onfoot outrunning crashing Derelict), or is the site-Mound blown up(by humans or SJs)?
Is Shaw away from Prometheus when the fight with infected Mohawk guy breaks out in the bay?
Is Prometheus ramming the Derelict just to prevent Derelict from leaving, or is there a duel purpose of Prometheus already being infected?
Once the Prometheus rams the Derelict, I am assuming there are no further scenes that take place in human hallways. "Prometheus has landed" makes it seem like there is no other ship in orbit. One scene in new US trailer shows blast shields folding away from Prometheus cockpit, while it is still in space.
What angers the SJs? The crashed Derelict rammed by Prometheus?(Yes, likely.) Or is it the taking of the alien-goo(taking fire from the Gods)? The goo is just sitting there, ready to be interacted with(possibly the SJs want the goo to infect).
Are the SJs ever non-agressive towards the humans? Are the humans just freaked out/scared in a few scenes, until the SJs are genuinely pissed off(wrecked Derelict)?
When did various civilizations learn the star chart? Were they visited?
Is the Mohawk-guy's helmet melting due to flamethrower(less likely) or because alien-goo canister blasted him in the face(fits with Face-hugger theme)?
Is the container that David is pulling the larger alien substance out of, the same shape as the containers at the Mound-site? I see markings on the side, but it seems a more cylinder shape, and pale in color.
"Big things have small beginnings" is said by David, with his finger out of focus. Initially I thought it was just a gesture. Look closely at tip of finger. Is that something small there? Alien-goo?
This is a super rough list, just to help me put stuff on paper, to start organizing it. Does anyone have additional comments to add? Disagree with the order? Did I miss a scene(not counting scenes before they arrive at planet)? Help me blend my three continuity-lists together.
I think the leaked script mentioned a few details I have not yet seen(my memory of script is faint, though):
A SJ behind the large statue-face.
The Gods/Engineers/SJs are please that their creations(humans) have returned to them, and take the humans deeper into the universe to show off their other creations.
Other misc notes:
"Something in my throat!" is said in main US trailer, but I rarely see it mentioned here on this site. It is amid the voices being played when Shaw is full of emotion and clasping her hands together.
"THEY are leaving" indicates more then one Space Jockey. "Where to?" "Earth." David seems to be making this comment from the star-chart room that is evidently not inside the Derelict ship that is about to take off.
