Okay, I'm very curious about two things.

Thing A: Where the heck has the Rapier been for six years? I really doubt it'd take the Jem'hadar that long to capture the ship and take it the rest of the way through the wormhole. Likewise, the crew doesn't act like they've been prisoner for six years.
Thing B: The Vorta is the same you meet in the 2800 series. Yet, you don't lay a FINGER on him in Rapier. Why does the next one accuse you of violently murdering his previous self?

A. They can't take a ship thats been time displaced. Which is why the crew doesn't act like six years have passed. For them, it hasn't.

B. I assumed it was an undeleted line for an event that didn't make the final cut previously. Or just an oversight.

When do they say the ship's time displaced? And why would the Prophets/wormhole aliens do that to the Rapier.

It's never said explicitly but that's what I always assumed, myself -- that the ship had been shifted through time by the Prophets (or at least the wormhole).

As to why it would have happened? No solid answer there, either. To be fair, the Prophets seem to have an agenda all their own. Makes me ponder doing a Foundry sequel to attempt to explain it, though...

And I'd been wondering that about Eraun, too. I didn't recall killing him when I played the mission. I actually can't remember what happens to him, it's been a while since I played. I suspect it's more of a case that his recovered memories of the incident are incomplete, so he assumes you murdered him. My best guess is he dies when you and the Rapier are blowing up attacking Jem'Hadar ships on your way back to the Federation side of the wormhole (in which case he's just being weaselly, since he would have been trying to kill you first).

That is one thing that's been deliberately vague, is how clones of Vorta gain access to the memories of their predecessor. Since we've seen it happen in other situations where there was no body (and thus no brain to read engrams from) to speak of (I believe the first Weyoun clone we see on screen gets vaporized), I figure there has to be some sort of telepathic mechanism that transmits the memories to be inserted (somehow) into the next clone before it wakes.

I always got the impression that the Vorta blames you for his last clone's death because his failure at his own mission resulted in him being killed when he got back to the Gamma Quadrant, and his current clone took over.

There's also cases of multiple vorta clones active at once. Two Weyouns talked to each other when the one defected.

As for Eraun... He surrendered to you basically, and knew he failed. It always seemed to me that he stayed on the Rapier and went back to ds9.

Yep. It's also probable that he activated his termination implant due to you stopping the Jem'Hadar from taking over the ship.