Can u leave a link to the site so we can take a look. With that many changes u may want to find a theme that is closer to your needs then it would less to work on.
1) do u want only home page to be with no side bars and full width?
2) Read me txt can prob be taken out of the php. .U dont want the excerpt to show on home page .. u want the whole post to show??
3) If i understand you right then u can try to use the “appearance>menus” to create a “custom link” to where ever you want such as you “shop” offsite.
The changes sound easy but it is many steps to fix all this so that is why it may be easier to find theme closer to your end wishes. Not to say we cant get it all good but it just may take some back-n-forth here. It is not the easiest thing in world to type out thought and instructions …at least not for me … lol but i try!
Oh , this is page 3 so go back and read thru the 1st 2 pgs, u might get some ideas. Nav is below on right (…if u havent read it all already.)