You usually do not want to set motion_velocity equal to come value (unless maybe to make it stop or to adjust gravity on the floor). In general you should be adding or subtracting from it. This is because the motion_velocity is a variable that is handled and may be modified by the physics engine. So it's not exactly your variable, it's part of the engine that you have access to.
So in your case, you might want to do something like this:
motion_velocity.y += 400
But you have to be careful, because your other code is setting the y to zero (like if you press left or right). So if you are holding left, and press jump, you set y to 200, and then the next frame set it to 0, which will remove any motion. So you need to restructure the code so you are adding and subtracting, not setting hard coded vectors.
