"I'm in a discussion with a couple of guys on another board who think we'll save nothing or no better than a factor of 2 in costs and safety with the shuttle derived HLLV and CEV launch vehicles. From what I've read I was under the impression the new architecture would be far cheaper and safer. "
I agree, if the assumption is that NASA has to build and operate a rocket that can do Moon missions and other things.

"I know this stuff hasn't been developed yet but can the booster-based CEV launcher be as cheap as a Ruskie Soyuz (around $50m I believe)? Won't the HLLV be far cheaper than a shuttle launch? Any idea the costs of launching 100+ tons to LEO on the in-line HLLV?"

The Soyuz is one of cheapest launchers in the world, other than chinese rockets, Sea launch [which is modified Russian launcher launching from only major private launch site]. So your question really is can NASA build and launch rockets as cheap or cheaper than the private sector.
Personally, I think we should first try out with making automobiles- how can the govt do any worse than the big three? And we get rid of those SUVs.

"Putting the CEV on the top of the rocket makes it vastly safer than the shuttle, but by how much? 10 times safer? 100 times?"

Depends on what you talking about- the whole safety of the launch system or within the first minute of the launch. There isn't enough data to give a reasonable answer. You could say the Shuttle system has killed 2 crews, and Soyuz system has killed one crew. The Russians have saved one crew from a launch explosive. But I think that is the only case of this escape system actually functioning to save the crew.