OP, I seat and crimp in one action. Try chamfering the inside of the case mouth just enough to remove the sharp inner edge. Increase the amount of flare slightly, 1/8 - 1/4 turn on the flaring stem. DO NOT overcrimp. That should take care of the shaving.

As others have said, the case bulge at the base of the bullet is normal. You're swedgeing the case to a smaller size and then stuffing a larger bullet into it.

I know I'll irritate some folks, but you could have done better than Lee dies.