As we know just because a person has more mass that doesn't mean they can lift more weight or punch harder as those actions are more about training your technique. My story is a martial arts / superhero type and I have seen "power ratings" or rough measurements of spiritual energy like chi and chakras being used in other stories. I was wondering if E=MC2 or other equations could be used to measure a fighters potential, not their resting energy but their max capability for single or short bursts of action .
Well, maybe. Sort of.
The idea would be that when acting as a superhero your protagonist's actions are powered not by his mundane physiology, but by tapping into the (chi, etc) spiritual energy produced by his body. Probably the closest approach to this is the Star Wars midichlorian bodies, which while biological also allow tapping into the field that is The Force.
Of course, relating this to body mass has its problems. First, the unit of energy production would presumably be the cell, and not all cells have the same mass. Second, this would require assuming that every cell in all magic users has the same efficiency in producing Chi energy. Otherwise, you can get someone like Luke Skywalker who has a very high density of midichlorians and much stronger Force than others of the same size.
Alternatively, your "midichlorians" might work by actually converting the mass of the cell it inhabits to effects such as powering a fist, with a conversion rate of energy to mass consumed being some factor of the e = mc^2 equation. Since individual cells in the body are not immortal, a certain amount of early cell death due to using superpowers would be acceptable, similar to the cellular damage incurred during heavy exercise. Note that, since you are invoking "spiritual" force, the rules do not need to be exactly the same as for mere material processes.
If you know the mass of (e.g.) your arm, you can apply the equation and discover what energy would be released if the mass of that arm were converted entirely to energy. But what's the point? It has nothing to do with the force applied swinging that arm. Therefore, you have a measure that's no more valuable than simply reporting the arm's mass and yet a whole lot more confusing because no one would know what you meant.
Your arm, for example, is accelerated via muscle contraction. After that acceleration has completed, (i.e., after you know the final acceleration of the arm) you could then apply the equation for force (F = mA) to derive an energy value. The same is true for legs, head butts, etc.
Which is what people do using tools like accelerometers to measure force-of-impact. (See our sister site, Martial Arts.SE, where a question about measuring force-of-impact was posted and the answers include ways to do it from cell phones to professional equipment.)
But even this is used only as a basic measure. Arms and legs are usually still accelerating when they impact the opponent. This means you can't measure the delivered energy without tracking the acceleration of the arm moment-by-moment. Each impact would be (and will be) different based on the circumstances of the blow.
In the end, F=mA is the basis used today to do specifically what you're talking about, but the data is aquired in far more practical ways: like hitting the bag attached to a tool designed specifically to measure the impact force.
And remember that it's force, not energy, that you really want to measure.