Fixing Rig Breaks Animation

[swift yoke]

ive run into a huge problem with a rig! turns out I animated nearly 1000 frames with an incorrectly rigged model and didn't realize it until i made the character look up, making his neck stretch weirdly. I also scaled this rig up a lot and forgot to apply the scale so im not sure if that's what's causing my problem, but when i try to adjust the ref rig, the animation is ruined. All I move is the neck bone, yet what's affected the most are the hands and hips? I don't get what im doing wrong unless it's entirely bc i forgot to apply scale

this is what the pose is supposed to look like, the above is what happens after fixing the neck

here's what looking up looks like without fixing the neck

here's how badly the neck bone is placed

i can't believe i never noticed 😭