The physics in this game are real wonky, and I don't envy the situation you're in with them as I've had endless trouble getting Unity's physic systems to work how I want them to. Whether using 3D (Havok) or 2D (Box2D) in Unity, getting them to work right is far more art-form then most programmers like to admit. There's a really great lecture on the finer aspects of managing either physics engine in Unity at https://www.gdcvault.com/play/1021921/Designing-with-Physics-Bend-the.

I've had limited success in 3D with forcing manual movement calculations into a Rigidbody.Moveposition() in a FixedUpdate() while having Rigidbody components with fricton-less physical materials and in worst case scenarios making their velocity Vector.zero every FixedUpdate, but that's not a great fix. XD

Edit: A sidenote as I had an issue with it, make sure that if you're using physics to move your player character that you also have any fancy-smoothed camera movement also happen in FixedUpdate() to prevent the character jittering. Update and LateUpdate won't sync quite right. Sorry if I'm being redundant or unhelpful. xD

The collisions on the player weapon seem a little wonky. It seems every time i play my attack stops connecting after the first two hits or so. I dig the music though, classical is awesome!