So I was trying different sizes of the main custom character and came through a problem, the animations did not replicate correctly.
Below is a combo animation on the main character, followed by the same animation on the secondary character.
I’ve noticed that the ‘Hands’ in the second character are not movable for some reason, might be the cause?
Everything is un-anchored but the HumanoidRootPart
EDIT: Solved by rerigging the hands with the LowerArms.