Hi there JC,
So to break it down, it seems like the base issue you are dealing with here is how to act, in a certain way, if free will does not exist. You seem to have summed up up the free will issue in these posts..
J C:
Put another way, if there is no separate permanent self, and if all things are subject to dependent origination, cause and effect (that is, determined by the past), there is no possibility of free will, which I define as: you, as a self, freely choosing between two possibilities of how the future will go. Your actions are conditioned, not "freely chosen." Am I wrong?
Quite frankly I would say you are wrong.

You may not be able to control the thoughts you think, or that you believe them to be solid, inherently existing, and capable of satisfying you, but you can choose whether to do or not do an action. This is essentially the basis of morality. By abiding by the Buddhist moral code of the 5 precepts, one chooses not to engage in certain actions. This is connected with developing mindfulness and ceasing to be overrun by your thoughts, or believe in their objective reality.
To review the 3 characteristics, they are: Impermanence: that phenomena has no fixed and lasting form, Suffering: that due its fleeting nature phenomena is unable to provide lasting satisfaction, and No-Self: that no phenomena is inherently, or self existent, or 'exists from its own side". These are somewhat different from what you listed.
You also said
J C:
So you can't control the self. You can't control what any of the aggregates are. Thus, no free will.
Woah, woah. Alright so just because we cannot control our thoughts, or our 'self', doesn't mean we have no free will. Think about it like this..
As Buddhism teaches, everyone has Buddha nature, and the potential to become enlightened. As well, from the perspective of an enlightened being, everyone is already enlightened. The purpose of the path is to overcome our delusory belief in our own separateness. From the enlightened perspective, the human race is a bunch of souls bound in physical bodies, stuck in a belief in separateness. Everyone has freewill, but problems of action are compounded by the mire of solid conceptual belief. This is not so much an issue as it is simply the situation in which we find ourselves. So to sum up, everyone is a spiritual being imbued with free will, mired in a belief in separateness.
The self has no inherent existence. It is simply a belief we formed and continue to hold on to. Clearly, we cannot choose or control our thoughts, and thus we cannot control the self. However this is beside the point of free will. The self is merely a delusion to which we hold dear. Try to imagine it within the greater context of our being spiritual individuals. For example, after enlightenment (something you asked about) the belief in separateness is gone, delusory thoughts are eliminated. However one is still on a path of spiritual development, the scope of which extends so far into the future it could be said to be infinite. The choices we make through free will: choosing to perform or not perform an action, are the cause of our growth. This can seem somewhat to be almost predetermined, but this is not how it is experienced, and thus it is a useless mind set to adopt.
As for karma and it's effects, that past actions affect our current state of being does not prove a lack of free will. In meditative terms, karma seems to refer to those thoughts which occur in our mind, "those ripening seed which have been stored in a cosmic storehouse." It is this which is eliminated upon enlightenment. The way one overcomes these thoughts is to release them and see them as false. This again points to our having free will.
When in meditation, we build the ability to recognize our thoughts as delusion (ie having the 3 characteristics), as things which do not form substantial basis for action. In some sense we could be said to be cultivating free will, or the ability to chose between acting on a thought, or not acting.
So the point of the three characteristics is that they may lead us to see that our conceptions are not as solid, inherently existing and satisfactory as we think. Keep in mind however, that without insight we naturally see our thoughts as solid, inherently existing, and satisfactory. This is why we cling to them, though in truth they are illusory, without truth and utterly unsubstantiated. So you don't have to force your mind to 'see' the 3 characteristics in sensation, merely remember that you should try to see this. If you see this you will have developed great insight (i.e. 4th path).
As for reconciling these three characteristics with morality, imagine this. Our ultimate self, our soul which is fixated in the delusion of separateness, is one with all, it is a part of the great whole. This is what it means that all are already enlightened. You exist in the state of wholeness but believe yourself not to. Essentially, when we commit negative acts this harms us on a soul, or higher self level, because as we are ultimately one with all, when we commit negative acts, we are in some sense harming ourselves. It should be obvious to you in a practical sense that you feel better when acting wholesomely that when acting with bad intent. When acting with malicious intent, our being seems to be taken over by revulsion for what we have done, our mind races, we cannot concentrate. When we act well and morally, our mind is much calmer, we are happier, we can meditate more easily.
This idea is the basis of the 3 fold path. Morality forms the base. Upon this base of moral action, our mind is calm enough that we can begin to develop Concentration. Then with this concentration, we can begin to develop Insight. Thus morality is the base, and insight the peak. Your question seems to suppose insight for morality, but on false pretenses.
Bit of a text here, but hopefully it helps. Cheers!