I remember the first build I had done and understand your questions, you are in a good place to get great help from people who really want you to succeed.
I think something in addition to reviewing these listed books, is to look at as many pictures as seems right for you to get a good idea of the exact type of rifle you want...the lines, the length of barrel, caliber, etc. There are options beyond belief, at first overwhelming, but with a bit of time you will find something that tickles your fancy.
Look up flintlock images and save any pics you like for study. Practice before doing anything new (if possible).
I think for me my best indicator is patience (or the lack thereof). If I feel like I am beginning to rush, or "can't wait to see how this will look" I know to stop! I can anyways come back and pickup where I left off, but I cannot always undo my goofs. (Although I do try to learn from each of them...)
Enjoy every aspect of your build. Chambers is a top notch company to work with. No such thing as a dumb question.
I cannot see from your note if you have a roughed in choice yet...any style you are leaning towards???