The first step before responding to your points below is to clarify that we’re talking “styleâ€ here, not “right and wrongâ€ issues. There are many styles (APA, MLA, AMA, Chicago, Harvard, AP, etc.). Believe me that if I could issue an edict that required all editors to use only one style, I would do so.
The goal of my notes is to get some style standards specifically for you that we both agree on. Also, remember that the writer/editor relationship is not a democracy. The voting rights are Author 51%, Editor 49%.

1. Not italicizing verses: I have been doing this for years, so this is a big adjustment, but I will take your professional opinion on not doing this if it makes it better. Thank you. 
I initially changed to lead-in biblical quotes to Roman type, then changed my mind and put the italics back in. In the running text, I prefer not to italicize long quote because, for me (and therefore presumably for many others) reading the text is more difficult (for example, a typo such as an “Iâ€ left out of a word is hard to catch when the other letters in the word are slanted). If you are accustomed to using italics, then please do so. I’m supposed to adjust to your style, not vice versa.

2. No edits need to be made to verses. I copy (& triple check) them directly from the Bible, so I'm thinking my content needs to be true that that. 
Yes, I just wanted to point out that editing already printed verses reduces your credibility. The ancient scribes probably made mistake and we don’t want to continue that tradition of altering agreed-upon primary sources. Of course, if I see an obvious error, I’ll fix it and certain add a comment about it.
3. In my copyright, I mention the version of the Bible unless otherwise noted. Is this sufficient? Or do I still need the translation noted on the first instance of a verse?
Good. Glad it’s in the copyright. I suggest adding it after the first quote, then you’ve given clear credit and need not repeat the source for every quote.
4. Pg. 5 first bulleted list there are no periods, second bulleted list there are periods, and then page 9 has periods. Which is right? 
Don’t have the text in front of me but my intention (and a standard practice across most styles) was to put periods after complete sentences and to omit it (leave it open) after phrases or incomplete sentence.
5. I am a designer too and I was pretty much thinking that the & in the titles would be used as part of the design in the book layout... but I don't want them to be used incorrectly... is that incorrect to use even for a design element? 
This is an author’s decisions (51%) and I can accept it, if you use the & consistently in all titles/subtitles. 
6. Church vs. church. This is my thinking behind this... When I'm using the capital C for church I'm referring to the global Church. Lower case I'm referring to a local body or assembly. Is this confusing? And suggestions?
That’s the way I understood it and I agree that you thinking is appropriate. Now, we need to double check and be sure that this pattern is consistent throughout the text. As you probably noted by now, “consistencyâ€ is the editor’s watchword. Inconsistencies are like speed bumps and slow down the reader or cause the read to stop and wonder why a word or phrase or design element on page 5, for example, doesn’t match the same word/phrase/element on page 42. 
7. Jesus's vs. Jesus' - I thought when something ended with s, you only needed the ' not the 's. I see you marked that in my text. Is this a style preference or am I using this incorrectly? 
I knew this would spark a debate. I found this explanation online and it discusses the issue better than I can (and after reading it, it’s still your call:
The most useful rule — and the most general and the easiest to remember — is simply that you add ’s whenever you actually say an extra /əz/ at the end when forming the possessive, compared with how you say the non-possessive version. Let your own ear be your guide. That’s all there is to it. No fancy rules full of exceptions. Just your own ear (as a native speaker, mind you).

In previous ages, some people did not add another /əz/ if it already had one, and so wrote Jesus’ to indicate they did not say an extra /əz/ there compared with Jesus: both are just /ˈd͡ʒiËzəs/ However, most people today now say Jesus’s, because it has three syllables: /ˈd͡ʒiËzəsəz/.

Same with Moses’s with three syllables instead of the older Moses’ with just two. Note that things like Ross’ and Chaz’ are always wrong, because no one says those with only a single syllable. That is a common error.

So it’s your boss’s house, because it’s got an extra syllable when you say it. Similarly, all the Jameses I have ever personally known have had the extra /əz/ tacked on when you are talking about something of theirs, which means it is for those speakers James’s house, albeit all the Jameses’ houses, because nouns are only allowed one /əz/ inflection, not two.
In all cases, the best thing to do is let your own ear be your guide, because writing should represent speech. That means that if you say an extra /əz/ then you write ’s, but if you don’t say it, then you don’t write it. That’s why you from time to time see forms like for goodness’ sake or for conscience’ sake. Those are possessive, but have no extra syllable.
 
8. You had a question about this in the style sheet: "Capitalize He, His in references to God and Jesus, except in Bible verses?" That is correct, I guess I've always capitalized He and His. Is this correct, what is your suggestion. I want it to make sense for the reader and not trip them up.
It’s correct if we agree that it’s your style. I think I noticed these pronouns were not capped in the verses but were in the text. If that’s the style, then we need to be consistent. Obviously, you have two other options: lowercase all or uppercase all. (Actually one more option would be to cap in the verses and lowercase in the text, but I’d rule that out.)  
I think the answer is to be true to the source Bible and to yourself (cap in text).
Also, in your experience do you recommend several passes of editing or do you feel confident that most errors have been identified? I want a good final product so I am open to the possibility of this needing a second pass. I just wanted to hear your thoughts on this. Again, thank you so very much for the excellent work. I will write a review for you. Thanks, Juli
I teach English class at a local college and during the very first class I introduce the Writing Process: brainstorming (getting your topic and then your specific thesis), writing the first (rough) draft, revising, revising, revising (as many times as needed), editing, and finally proofing. 
While I am confident that most of the errors have been identified, every time a text file is opened and changed, the possibility of new errors (I call them gremlins) sneaks in. All text, no matter how finished the author thinks it is, would benefit from additional readings by people the author trusts. 
After you make all the changes resulting from this note about style points, consider making several copies of the draft and asking friends to read it. The more, the merrier. If you are still uncertain about the text’s finality, or have any questions about whatever your readers find, then of course I’d be happy to do a second review.  

Hope these comments are helpful. Jackson