Thanks @Tex2002ans!
and everybody! I think I'm following most of what is being suggested, but it will take time for me to digest it all...
I knew there was something like rt-click-->replace trick. I will rename the classes, etc so it will be easier to figure out where they're being used for.
I think I have at least all the book text fixed.. so it's readable in Kindle
now I'm doing minor tweaks, but otherwise, I think all all is well.
Thank you everybody for all your help! I love formatting things (learned large doc formatting using LaTeX, so... this is so much easier) and intend to learn more eBook editing by trial and error.