(2D) What is the best way to implement a run-and-shoot animation?

Having a running animation transition to a different running-while-shooting animation isn’t working properly since the character’s feet will get out of sync when switching between the two states.

Both animations are 6 frames each, the only difference is the gun arm being raised.

Placing the two states on different layers didn’t change anything.

How can I have one animation begin where the previous one left off?

Or am I better off replacing the top half of my character with a legless sprite? If so, how is that achieved?

You can use animation layers. Your run animation can be on a base layer and shoot animation on another. shoot animation shouldn’t move legs of your character, only hands and a gun. Check this tutorial for more details Controlling Animation - Unity Learn