I'm getting 3 different scores: Intrinsic Motivation, Extrinsic Motivation and Amotivation. Is there a way to obtain one single score for Academic Motivation?
These are three aspects of motivation, as proposed by Deci and Ryan in 1985 as their 'self-determination theory'.
Deci, E. L., & Ryan, R. M. (1985). Intrinsic motivation and self-determination in human behavior. New York: Plenum
They have a retrospective on this in Contemporary Educational Psychology 25, 54–67 (2000) doi:10.1006/ceps.1999.1020.
Your question amounts to whether or not one can 'boil down' these aspects of motivation into something like the same thing. There are three problems with this.
The first is that you'd have to make a decision on the relative importance of each for the matter you are investigating. It isn't obvious that amotivation should count for just as much as intrinsic motivation. But maybe it's only worth half, maybe it should count account for twice as much. You don't know.
The second problem is that aspects could be orthogonal. That means it doesn't matter how much intrinsic motivation a person may have, if they have zero agency they won't do anything. Ryan and Deci think of them as basic and distinct needs so maybe they would not agree with this but I'm addressing the general question you are asking, about coming up with one score to represent the information you get from several scales. If one were to draw an analogy with the needs of a plant, you'd know it's important to think about sunlight, water and nutrients. They all matter for survival and growth, that's for sure, but having a single number to represent those different things might not work. The plant could have all the sunshine and fertiliser it needs but without water, it's going to die.
The third thing is that scales are often validated in order to make one study comparable with another. Trying to come up with a composite score means you couldn't do this any more. Your work should be a contribution to the research community (and world) you wish to communicate with so it might seem like a small point but it is important too.
Lastly, I encourage you in your work. It might be you see another matter for learner motivation, not easily accounted for by the scales you have used. Deci and Ryan are not an oracle, nor indeed are any scientists. They have presented a perspective on motivation, linked to the studies they and others have done. Your research may be probing motivation in a new way and so you may feel you wish to augment the scales that map onto their perspective with another that gets at a different matter again. Perhaps, if you go with the plant metaphor, something like pollination for the propagation of the species.