A way to here others horror stories. Don't mean that is a bad way. Just very enlightening.
It's not really a horror story. NYUSUK is taking some preventative measures, and it's a good idea, but the visa itself is not in jeopardy.
A simple overstay in itself is not sufficient grounds for refusing a spousal application (if there's been no prior removal actions), the application is for settlement after all, right? If everything else about her app is in order, she's a happy bunny. However, there's lots of gray areas downstream, and lots of things can happen before she starts waving a British passport in the air. Mobility in the EU, subsequent apps, changes in the rules, lots of unknowns.
And the only thing governing all that is what gets put in her transcript that the ECO makes. And sometimes it pays to be safe and get your own explanation included in with it - because it can affect your credibility later. Of course it's optional, and certainly if you trust the ECO to get it down correctly or you are confident to clear any issues arising in the future, then you can ignore it altogether
Maybe some people lurking out there who got their spousals and then refused their ILR might shed more light...
About your idea for a manual or book, I was reading a series of books earlier this year for American spouses abroad. They were about $15 each and I think 6 or 7 of them. They covered stuff like how to improvise 4th of July house decorations, or what to do if your oven is (heaven help us!) too small to make a Thanksgiving turkey. OH! And the British are very economical, and you will fit in better if you grow your own vegetables - and you can get good tips from your neighbors.
And OMG! Don't wear heavy make-up in Arabia! Stuff like that.
