Just use a hone from super cheap.
some wd40
Hone the least amount you can to get it to come up reasonable.
If theres still a few of the deeper marks left dont fret.
Yeah its a precision instrument, but its not, its pretty rural technology, but its robust and hardy and that leaves lots of room for error or forgiveness.
If the crank bearings are OK you do not need to remove the crank.
as for the crank pin. Im a bit under the pump but i will see if i can put up a post about that.
A light hone, a piston cleaned up with some wet/dry, new rings, it might not be 'in tolerance' but it will still do the job and do it vastly better than what it was before with a beat up bore and scratched rings.