1) t would be nice to jot down a "More Permissions URL" for anybody who wished to obtain information about clearing rights that are not cleared by my license. I would imagine the easiest way to do this would be to use the same URL as I would type in for "Attribute Work To URL" - which is, simply, just my website.

An alternative that I use is a separate license page, which is linked from the main page.

2) Is it unwise to use the e-mail address that I used to register with WordPress.com? Or should I just create another e-mail address that is specific to the aforementioned inquiries? Or - is this just not the best thing to do at all?

I would never put a permanent email address on your website, it will get hit by more and more spam as time goes on. I use a temporary address from Gishpuppy that I change when i get to much spam. Another alternative is the contact form

3) I attempted to go over the whole "Google Apps" thing, but in light of my exhaustion and the ostensible complexity of the whole ordeal - not to mention the fact that I truly don't understand what I am to gain by the whole "e-mail and domain being together thing".

If you don't need or want it then don't do it! It is fairly complex, though the instructions are good. Personally I do have some @my-blog.org email addresses because I sometimes post to lists and people as the blog owner rather than using my personal email account.