Does the shape and mass distribution even matter? It's going to have a center of mass, so once that's located, shouldn't the orbit be close to a perfect ellipse?
Yes, mass distribution and shape have a huge effect in the orbits.
For example, the perturbations from Earth's equatorial bulge causes the perigee of an orbit to shift eastwards (see: Molniya orbit). The Moon's gravity field is very irregular and orbiting the Moon at low altitude is just black magic.
The issues is that, technically, orbits aren't stable in the sense of being described perfectly as ellipse with a point mass at one focus.
That approximation can describe an orbit for a while, but after time the position will differ from the predicted orbit, until at some point you have very little idea of where it will be.
A Rosetta goal now is to figure out the comet's mass distribution, so that the orbital predictions can be better. The orbit won't be "stable" but it will be more "predictable."
Even then, we expect Rosetta to release gas, dust, and water vapor which affects the orbit. I expect there will be orbital corrections over the next few years.
tl;dr: no, it won't be a very stable orbit for very long.
One definition for the "stability" of an orbit is that if you give the orbiter a small nudge, it will not radically change its orbit. Lagrangian points L4 and L5 are not stable (with this definition) while L1, L2 and L3 are (only in theory, though, in practice perturbations matter a lot).
Since the mass distribution is unknown, we can't quite predict if the orbit will be stable or not. The mass distribution may be very uneven and there may be spikes in the distribution (due to shape and porosity of the comet) that could cause the orbit to be unstable. The comet also rotates and makes things more difficult.
Now the goal of the crew is to find an orbit that is reasonably stable and predictable given the knowledge of mass distribution they have. Nevertheless, the space craft will probably have to do thrust maneuvers to stay in orbit around the comet.
And once the comet comes close enough to the sun and starts to lose mass to the vapor trail, all bets are off. That almost certainly implies some kind of unstability due to mass changes as well as the drag from the vapor trail. The comet may even break down to several pieces when it comes close to the sun.
If a comet breaks up into several pieces, will those pieces continue to travel next to each other in the same direction, maybe re-combining via gravity back into a single rock? Or will they just drift apart?
Depends on how fast they are ejected from each other. The pieces will (more or less) have an "escape velocity". If they are faster than this velocity they will drift ever further apart. Slower, and they will slowly fall back towards each other.
My understanding is that it's unlikely that they would ever recombine into a solid object since the gravity between them is so weak.
Another definition of "stability", perhaps more relevant here is: if you complete an orbit without crashing into the body you're orbiting, does that guarantee you won't crash into it later?
When orbiting a uniformly-dense sphere in an otherwise empty universe, this holds. When orbiting a body that approximates a uniform sphere in a universe where all other large bodies are relatively far away, this mostly holds. But significant deviations from a spherical shape can easily make most orbits unstable.
Little known fact: the Earth's Moon deviates enough from a uniform sphere to make long-term orbits tricky. Wikipedia article:
Nice bit about a small satellite released by Apollo 16:
"Instead, something bizarre happened. The orbit of PFS-2 rapidly changed shape and distance from the Moon. In 2-1/2 weeks the satellite was swooping to within a hair-raising 6 miles (9.7 km) of the lunar surface at closest approach. As the orbit kept changing, PFS-2 backed off again, until it seemed to be a safe 30 miles away. But not for long: inexorably, the subsatellite's orbit carried it back toward the Moon. And on May 29, 1972—only 35 days and 425 orbits after its release"—PFS-2 crashed into the Lunar surface.
And this is all without any of the additional trickery coming from outgassing.
It's not so much the shape of the moon but the mass concentrations. The moon has significantly stronger gravity over impact basins. Based on shape alone (low plains) you'd expect lower gravity there.
For example, the perturbations from Earth's equatorial bulge causes the perigee of an orbit to shift eastwards (see: Molniya orbit). The Moon's gravity field is very irregular and orbiting the Moon at low altitude is just black magic.