Hi again,@Carlmed00! Hope you had a nice weekend, wherever you are.
Regarding your other questions and observations, we've come to the point where all I can say is, "it depends." 
The answers to your remaining questions depend on a variety of factors that are specific to your study and data, so unfortunately I can't answer them for you. I think you are headed in the right direction with the questions you are asking though.
EDIT: Please see Technical support re: Illumina want to use only forward reads for some discussion on this topic which you might find helpful, @Carlmed00.
Best of luck!
Andrew