That can be done in 2 ways...
you can either go into the original (the 'lego' model) of Cloud, and adjust the bone length of all his bones until you have it 'right' for the model you want to replace it with.
Now, this itself is a decent way as now, the individual file parts move at the joints instead of halfway down his arm or something.
or, you can go into all of the animations, and change them to be more realistic, which i admit is needed for some animations, such as the idle standing one.