Damn, don't you just hate it when that happens...
It may not be as bad as you think.
1) The crank and the inner bearings are the main issue here, if the inner bearings are not rolling smoothly, you shouldn't take a chance, to change them, the crank will have to be split, that's gonna cost ya.
It might be cheaper to just get a new crank... Can you say stroker??
2) I don't think the crank would have been damaged, just to make sure, take it to a machine shop and have them check the run-out. (0.05mm or 0.0021in max)
3) As for the cases, bolt them up dry without the crank and measure the bearing landing face to see how much ovality it has (check to see if it is still round) if you don't have an inside micrometer or vernier, take it to a machine shop to have them measure it up.
4) As for the "little holes", what is little, and do they interfere with the existing holes?
If they are just dent marks you could get away with just cleaning up the burrs.
Let us know how it goes.