It seems to me that all the aspects of rectification are really the fulfillment of mitzvot, which are dependent upon the "limbs" of the Nefesh. All blemishes result from violating negative mitzvot.

All blemishes result from violating negative mitzvot

It is well known that there are 248 positive mitzvot and 365 negative mitzvot. The negative mitzvot tell us what not to do. Their number corresponds to the 248 limbs of the human body, which is made in the image of the Nefesh. Thus, each one of the negative mitzvot corresponds to one of the limbs of the Nefesh, and transgression of any one of them causes a corresponding blemish or damage in one of the limbs of the Nefesh.

Positive mitzvot, on the other hand, require a person to actively do something. They cause tikun (rectification) of the Nefesh.

Positive mitzvot… cause tikun (rectification) of the Nefesh

The complete entry of the Nefesh into the body, which is called tikun of the Nefesh, is accomplished only through the performance of mitzvot. Although sins blemish the Nefesh, they do not prevent its sparks from entering.

A person can perform positive mitzvot, and in the same lifetime transgress negative precepts. As a result of the positive mitzvot he will be rectifying levels of soul, one after the other. The sparks of the Nefesh will be entering the body and becoming rectified.

On the other hand, as a result of the negative mitzvot that he has transgressed, he will have caused blemish or damage. These will have to be atoned for, one way or the other, but they do not necessarily prevent the progress of tikun.

[Commentary by Shabtai Teicher.]