By the power of truth, I, while living, have conquered the universe.
I don't know how I missed that... wow. So Forerunner ships use engine drives for normal travel, getting from point A to B without slipspace. But the Crystals enable them to go into slipspace?
How did they find out about the crystals?
Possibly stolen technology from the Precursors? The Forerunners seem to be more like the Covenant now, imitative instead of innovative with technology. Considering the way it's described, it sort of fits the description (or the way I imagine) of a Precursor construct - NOTE: I always think of the shards in the Shivering Isles from TES IV.
Where are they?
All the Crystals come from a single core Crystal that only the Master Builder knew the location of. Where this is? We do not know.
Are they natural or precursor?
From answering the first question, I think Precursor would be more likely.
what if the supply runs out?
I'd imagine it would take a very long time for this to happen. They only cut out a tiny fragment of the Core Crystal. But still, if it ran out the Forerunners would have to work out their own methods of slipspace travel.
Did the covenant know about this?
I doubt it.
what did Truth do with the shards?
Both the UNSC and Truth possessed shards, but it seems that they don't do anything. Page 287 from First Strike says:
Chunks of broken crystal on the pad refracted the light and distorted her image so she appeared half melted and cast prismed arcs of light onto the walls.
...
Cortana faced the Admiral. "Sir," she said, "you'll be happy to hear that I'm detecting no signals, residual radiation, or any transient contacts... which is precicely what you'd expect from a normal Slipspace journey."
[Edited on 04.20.2011 6:17 AM PDT]