There should be three dowels in the crankshaft flange, not two. Unless the third dowel is installed, you will have a massive oil leak into the bell housing which will trash a new clutch in a matter of a few miles. You'll also need to put some type of sealer on the flywheel attaching bolt threads, (blue LocTite for instance) as those holes are also exposed to the crankcase and can leak oil, especially if the wrong type of lock washers are used on them. I wouldn't hesitate to run that flywheel- - - -just get it ground flat and ignore the minor cracks. I've run MUCH worse ones for thousands of miles.
Jerry