Reddit reviews Metaphysics: A Contemporary Introduction (Routledge Contemporary Introductions to Philosophy)
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Of course you can investigate them. The way I word it, there are four:
Now, Transubstantiation is an in-house debate within Christianity, so if you don't concede 1 and 2 at least for the sake of argument, talking about Transubstantiation is premature. So assuming that 1 and 2 are out of the way, it then boils down to rational investigation of the scriptures in 3, and rational investigation of objecthood in 4. I have this textbook which goes into detail about #4, and it can certainly be argued against as the author offers two competing theories, and therefore it is falsifiable.
Michael Loux has a good introduction to metaphysics: http://www.amazon.com/Metaphysics-Contemporary-Introduction-Introductions-Philosophy/dp/0415401348
Might as well weigh in on what you should focus on specifically, as one of those philosophically-inclined theists. As for why you should-- given that atheism and theism are both within the field of philosophy, it'd be good to at least have a clear view of the evidence for both sides. I'll be giving books that support theism, since I don't know many that do so for atheism-- something by JL Mackie might help?
Before even engaging in the philosophy backing theism, it'd be good to get some background knowledge.
Intro to Logic
Metaphysics
Given that, you can familiarize yourself with some books on classical theism, attacks on naturalism/physicalism/materialism, and specifically attacks on materialism of the mind.
The Last Superstition
Aquinas
Philosophy of the Mind
All three of those are by the Catholic philosopher, Edward Feser. I usually argue for theism, or against materialism, based on his books.
I don't think that is an especially good definition, since epistemology and metaphysics are separate areas. Though 'first principles of knowing' could refer to questions like "what is truth?" or how the world gives beliefs content, which would be metaphysics. To motivate my point, check out the table of contents of these standard textbooks:
Epistemology: A Contemporary Introduction
Metaphysics: A Contemporary Introduction
You'll note that your first three topics all appear in the former book and not in the latter.
Loux certainly thinks so (at least if I remember his book correctly).
Edit: Before we go any further I should any further I should say that metaphysics is my weak point, and I haven't spent much time on it.
I almost always suggest this one: Michael Loux - Metaphysics
http://www.amazon.com/books/dp/0415401348
It covers a variety of topics that are laid out in detail and is a good introduction for beginners.