Theresa, at some point, we should discuss house style and how it might affect an author's edit.
(House style is how a particular publishing house decides various editing issues, like in "the fall of 1999," is "fall" capped or not. Often, as with our house, these rulings are captured in a stylebook, which is available to editors and authors. Complicated editing issues are not usually dealt with in the stylebook, but it's very useful with those discretionary decisions in capitalization and punctuation.)
One thought I have-- the house style is not something a submitting writer needs to worry about. You won't even usually have access to the stylebook. So if you're faced with one of those trivial but knotty questions, like how many if any periods should go in "Ph. D.", check the Chicago Manual or go with your own inclination. It won't make any difference in acquisition decisions.
Once your ms is acquired, the house style becomes more important. And if you can get a hold of the stylebook, it's very helpful if you run through the ms again and make the changes needed to conform to the style. However, the stylebook is really more for editors, first, for quick answers to those pesky little questions, and second, to provide an excuse when an author is sure that deleting that space in Ph.D. will mess up her style. "Hey, that's the house style. Sorry."