Rather then scatter our requests for help with a book across all the training threads, how about if we try to post questions and requests for help here?
Again thanks for all your work. I see you've completed another book, and I haven't even updated the sign-up pages. It's pretty embarrassing to have you proofing entire books before I can update a line or two on our web page!!!
Here's my 'advice' concerning your questions and scriptural references. While our goal is to have CCEL's pages match the original pages of the book, this is LESS the case with foot notes and scriptural references. We'd STILL like the references to match, but there are numerous issues including the following. (1) Different editions have different references. Ideally, the CCEL book is the same edition used for proofing, but this isn't always possible. (2) The footnotes and scripture references are generated automatically based on the tag commands of the .xml file. Many of our proofreaders don't do much if anything with the tag commands, so it's not possible for them to fix issues with references. (3) Although we'd also like the references to match, there's virtually an unlimited amount of proofreading to do at CCEL, and we'd rather get the main text of the books proofed and skip the references than have our volunteers get very frustrated with this tricky issue and give up all together.
So, I've given you a very LONG answer that doesn't really answer your question at all. I apologize. You are more experienced at this than I am (having completed how many books?) so I'll leave it up to you to decide what to do and hope that possibly others here can provide their input which might be more helpful than my input.