Getting Real Page Numbers will require using a
Page-map or a
PageList and requires you actually publish it on Amazon; Kindlegen will only generate an index that Amazon can turn into the required .apnx
Page numbers are kind of meaningless in an ebook -- what size page is it supposed to correspond to anyway, in a format where the size of a page is user-controlled?
As far as where you start the book, it is controlled by a Sigil option -- right click on the html page where the book should open, select Add Semantics, and choose "Text". (see screenshot)