Thank you all for the thoughts; I really appreciate it.
I am curious why you all are saying Sigil is easier to use for editing than Calibre. They both seem about the same to me, so I wonder if Sigil has a feature I am not taking advantage of. I tried "Mend Code" but that did not seem to do anything. Honestly, all of the HTML functions just fine as HTML - it's just a matter of not knowing the proper epub syntax for some of it.
It seems that <div> </div> works in the blockquotes in place of the line break, though in Sigil with the Flightcrew plugin, I then received this error, which I had not gotten with epubchecker - "Error schema not satisfied : no character data is allowed by content model near column 157". This just refers to a </blockquote> tag, so I am really not sure what the issue is:
<blockquote class="calibre8">“—the vastness, profundity, and unsearchableness of His works, which have a depth in them greater than the well of Democritus."</blockquote>
Also, <span> did not work inside the blockquotes for italics. I think I am just going to drop the italics from any blockquotes and call it a day.
Maybe it would have been cleaner to just do this all in Word from the beginning using styles, but I thought the HTML would have been better. But at this point, with over 6000 lines of HTML, I think it is going to be easier to just fix the errors than start from scratch on the formatting. Most of it works fine. Next time, I'll use a paragraph style instead of the <blockquote> tag!