I forgot to mention this, but if Link is facing down when firing the sword beam, the sword beam animation is rotated at a 180 degree angle. And yes, this problem, as well as the other two problems mentioned above are still present in 2.50.1 RC2. As for the beam impact sprite offset, why not fix it to where the beam impact sprite comes after the last animation frame of the sword beam itself, instead of being offset by the number of animation frames plus 1.
And in future versions (in other words, a rewrite), perhaps it would be nice if we could define a separate sword beam impact sprite for each sword.