The objection you are raising is a common both among students and scholars with respect to Kant. Some versions of the objection are better worded and structured than others, and some versions seems to misunderstand Kant pretty badly.
I'm going to parse some pieces of your first paragraph here:
An example of heteronomy would be choosing what to eat, as it to satisfy hunger in the fullest, which is not an end that the individual has explicitly chosen to be subject to.
Yes, this would be an example of heteronomy for Kant. But it's important to realize that heteronomy is not per se immorality. For Kant, heteronomy happens whenever we commit ourselves to an action apart from what our own reason dictates we should do.
Here, it's important to qualify that by "our own reason", Kant does not mean "by using our own reasoning" if that is at all to mean that we would come to different conclusions than what he takes to be the one true form of reason dictates.
In any situation I consider, the human is bound by their desire to maximize their own pleasure (a heteronomous end), whether it's choosing the happiness brought on by "choosing" morality or making any other real world decision guided by an involuntary master.
Here, you are expressing what is a fundamental disagreement with Kant about what humans can do. Kant expressly believes that humans can using reason in conjunction with a free will elect to pursue an action on the basis of reason alone.
In the Groundwork, Kant calls the choice to pursue happiness "imperatives of prudence" and sees these as a form of hypothetical imperatives (perhaps the best form). The text is not super clear on what these look like, but it seems to mean something like:
if I want to be happy, then I should exercise regularly.
And then acting on that is heteronomous since the goal is contingent on an "if."
Conversely, he thinks moral ends are those dictated by pure reason and we act morally when we choose to pursue those ends for the reason reason supplies.
There are several different variations on the objection that Kant's idea does not work. One version is that to realize an end requires us to pursue it in the world (Hegel's objection). Another family of objection is to the picture of how we choose actions, specifically, whether we can act for multiple ends at once (this is considered in detail by Marcia Baron in Kantian Ethics Almost without Apology). A third objection group is to suppose that Kant's idea of reason doesn't really exist (also raised by Hegel among others; taken up by Habermas).
People differ greatly in how effective they think these objections are: Allen Wood started by writing about Hegel's Ethical Theory but by the time he wrote Kant's Ethical Theory he found the objections thoroughly unconvincing. Dudley Knowles (a Hegel scholar) did not think they were any good. Charles Taylor, on the other hand, seems to find them impressive -- at least in Hegel (Cambridge University Press, 1975).
A fourth objection is to simply assert that we always act for happiness. I think this is a poor route of objection, because it involves making a big positive claim about how people work. And if there's one empirical fact it is that people work in many seemingly different ways. Why go here specifically when you can attack Kant on other grounds?
Moreover, if we say people act for happiness, we to some extent need to figure out what we mean by "happiness" and whether this is closer to Aristotle or Mill/the Epicureans (i.e., does it have robust objective features or is it pleasure?).
Kant was not unaware of this (seeming?) problem with views. One unfortunate reality about most people's exposure to philosophy is that they only read the Groundwork. The Groundwork among other things takes a dimmer view of happiness than later works where Kant incorporates happiness as a part of the "complete good" (vs. the "highest good"). Moreover, later works do more to suggest that we can be concerned with the cultivation of our own virtue (See Nancy Sherman, Making a Necessity Out of Virtue).
Still, Kant never shakes the idea that the right thing to do is the thing reason dictates it, and the right way to do it is with the objective feeling of respect for the moral law.
One way that Kant tries to handle the fact that people always act for their own happiness is that Kant believes there is a good who will give people the degree of happiness their actions merits. This promise in part is supposed to enable us here and now to act morally -- since we don't need to concern ourselves with getting the happiness befitting moral action. This point echoes the Christian image of a just God.
Kant defines that humans are worthy of rights because of their capacity for autonomy
This could potentially be reworded to remove some ambiguities but is basically correct. For Kant, humans have rights because they are rational entities. These rights are metaphysically present whether or not they are realized on the Kantian view.
In your second paragraph, you are exactly right when you suggest Kant thinks our moral actions are different than ends-means action.
When you state the following:
If truly autonomous decisions are only made to fulfill ends or maxims that innately chosen in autonomy and choices even made out of moral consideration are made to satisfy one's moral compass (an end/maxim that individual did not choose but was innately given), how are any decisions truly autonomous?
There's an important piece missing here (or at least obscured). The phrase "innately chosen in autonomy" strikes me as problematic. For Kant, reason dictates the content of morality in the form of the categorical imperative (which Kant defines in multiple ways that work out to clusters around universalizability, treating rational beings as ends-in-themselves, and the idea of a community of such beings). But the basic idea is that Kant doesn't take this to differ by subject. Part of the problem is that the word autonomy has taken on a different meaning than what Kant meant. For Kant, what makes something autonomous is that the subject used their reason (a necessary and objective form of reason) to draw the conclusions reason dictates and then used their free will to follow the conclusions of this reason. (Contemporary autonomy literature has to balance the question of free choice against the sort of "innate" or "culturally-received" ideas of what to do).