Yesterday I wrote up a big rant about how we know there are some things that Ruin hasn't messed with. I made essentially the same points as Comatose made:
1) Ruin could not change too much too quickly. Normal people would notice. There was almost certainly a verbal tradition in addition to the Worldbringer's metalminds (people had heard the stories before). Anything that drew attention to itself was dangerous.
2) Even when Ruin did make changes, it had to make them slowly. If it could have, it would have almost certainly changed Kwaan's document to be less contradictory, more consistent. Instead, it focused its efforts on the parts that referred to itself explicitly. Given the fact that the contradictions almost led to it not being released, I think we can view this as an inherent limitation on the speed with which it could make changes. I.e. it could only make a few changes over the course of several months.
3) Kwaan himself notes that the changes were subtle. This supports #1 and #2 above. It's power was limited in clear ways.
4) Ruin is clearly not omniscient. It had to adjust the situation to the as it changed, and it didn't know how it would change. We can see this by the way changes to the "Hero of Ages" prophecy happened within Kwaan's lifetime to match Alendi---if Ruin could have seen far enough in the future, it could have matched Alendi well in advance. We also see this in the way Sazed's document was changed---it responded to events as they happened. Slowly.
5) Most important of all, it's power has not always been active in the world. Why do I say this? Here's the quote:
The prophecies have changed. They now tell Alendi that he must give up the power once he takes it. This is not what was once implied by the texts--they were more vague. And yet, the new version seems to make it a moral imperative. The texts now outline terrible consequences if the Hero of Ages takes the power for himself.
This is easily the most important part of the prophecies, the thing that Ruin absolutely had to change in order to get free. Surely it could have changed them without knowing the Hero of Ages, given that it groomed the "Hero" for the role? If it's power were as extensive as some of you seem to imply, these changes should have been the slowest changes, and done well in advance. Instead, the change happened within Kwaan's lifetime in a way he could notice. Thus we can conclude that Ruin only had a small window of opportunity to change the documents, and in fact it failed to get free that time because the window was too small.
From this we can come to some conclusions:
A) Ruin focused only on those changes most advantageous to itself, due to its limited time and ability. Most documents, even those that contradicted its version of events, were probably ignored simply because they didn't matter. Getting the hero to focus on its version would be the best use of its resources. Thus unless the prophecy needed to be changed to get Alendi or Vin to the well (or otherwise forward Ruin's plans), we can probably assume it is correct.
B) Most of the time between TLRer's ascension and MB2, Ruin probably couldn't affect the world at all. Most documents and metalminds from this time are almost certainly untouched.
C) We can probably tease out some truths from things that are sufficiently vague. There is no reason for Ruin to change them unless it sees a profit in it. Alendi's second-hand quote certainly applies here.
Thus I feel that we can make some predictions based on the prophecies. When we argue about whether something has been changed or not, the above considerations should be applied. I've been trying to find the time when Tindwyl and Sazed were discussing contradictions between different sources on the hero's height, but I can't seem to find them and don't have the time for a reread.
My $.02.
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. The "no woman may claim him" bit seems to work in a perverse sort of way as well.