1. Regarding the basis of philosophy, I don't think we are that far apart. As you said yourself:
I particularly appreciate your emphasis on practical rationality. Let me say, again, that when I start with being, I am not starting with my being, but rather, with being generally. That says nothing of whether or not all things are one or not (an issue that plagued the Greeks) . . . perhaps, at this stage, anyway, the post-moderns are exactly right in most of their challenges to our ability to really know anything. Perhaps everything is only a single substance. Fine. What, I think, is evident is that something exists, even if it isn't you. That leads to the question, "What do you mean by existence?" And that, I think, is where good philosophy starts. Let me put it this way:I do start out embracing "being", and I guess immediately thereafter myself. I just do not embrace my existence based on logical reasoning (which I don't see as possible), but rather I embraced my existence based on what I call a practical rationality. With a foundation to begin from, I begin reaching and accepting other conclusions.
The basis of philosophy is reality: that which is.
The first question is metaphysics: what is that which is?
The second question is epistemology: how do we know that which is?
The third question is linguistics: how do we communicate what we know?
The final question is hermenutics: how do we understand what we communicate?
The problem with Descarte--and pretty much all modern philosophy (thanks, in large part, to Kant)--is that it starts with epistemology. It asks, "What can I know?" But what is the implied subject of "to know"? Actually, Descarte is asking, "What can I know about reality?" because knowledge must be about something to be knowledge at all. Thus, you have to define what "reality" is, which is the study of metaphysics and being, before you can ask the epistemological question of how it is known.
In light of all that, I point out that the question of the nature of humans--what and how we are--is metaphysical and thus comes before epistemology. Perhaps much to the chagrin of many Christians, I don't think we need the first word of Scripture to understand what a human is, although I thoroughly expect Scripture to shed additional light. Such is the nature of progressive revelation.
Finally, on this, I see why you say you start with God. In the sense that you actually start with being, I can agree. A proper study of being leads necessarily to God's existence in that it discovers subsistent existence, which is a fancy way of pointing to your argument from contingency. I would, then, be interested in your thoughts on the above, as I think our differences may be in nuance and wording, not anything deeply substantial.
2. Which leads to substance. You are right that I don't agree that God is a substance, on which I am following Aquinas. For me, God cannot be a substance because "He is not the subject of any accidents, but also because in Him essence and existence are identical, and consequently He is not included in any genus whatever."
Now, I can understand, I think, why you take the view of substance you do. It's not too different from the classical definition, as that which "stands under" the thing itself and receives the characteristics and properties we call accidents. It is, in a word, fundamental, and the important idea is that it is in itself (unlike redness, say, which is not in itself, but in the substance). Descarte defined substance as "a being that so exists as to require nothing else for its existence," which I would expect you to reject, for the simple reason that, as a Christian, the only thing that requires nothing for its own existence is God. There are philosophical problems with such a definition as well, such as the fact that it leaves no room for efficient causality, but we can leave all that aside, as I don't think it applies to you.
For me, then, I don't see how a thing can be a substance if it does not have both form and matter, for matter without form is in fact no thing, and form without matter may be a universal, but certainly not an individual, and only individual things can have properties. That is why I don't see either form or matter as being a substance, but rather, a thing is a substance when it has both form and matter. So if you understand substance as something having both form and matter, I fall back on all my original problems. Your view seems a bit different. You say that substance isn't just form, but that forms themselves are substance, which implies that substances underly form. I can only assume that, for you, substance also underlies matter? I'm not sure, then, how you would actually define substance . . . "the thing that underlies form or matter" . . . or "a thing that can have properties," but then we fall back on the definition of "thing," which would be hard to define without referring to substance.
In any case, if you can work out a consistent set of definitions here, then I actually don't think I would have a problem with your view of substance dualism, as you wouldn't seem to require the soul to be a substance in the same sense that I would use the word, and, as such, it could almost be more like an aspect, as I have described earlier, though I don't know how you would feel about that characterization. I'm very much looking forward to your thoughts so far.
3. Finally:
Given the view of substance above, I think I can see what you mean by this, and can broadly agree. So let's leave off this thought until we clarify our terms.The body is a human body because it is able to interface with human form (or was able to before it expired).