1) add:
style="margin-top:10px;"
to the div that contains the paypal logo
2) the real test is to go back to the unchanged checkout pages before you added your design to it. test the pages before adding your design.
in all reality, most stores use a very basic page design for the checkout pages, no menus, or footers, just a basic header, a link to the home page and the checkout details. a full page design is not needed on the checkout pages, by having all the footer links and the main navigation and other bells and whistles, you give the customer more options to back out of the checkout process and abandon the order
6) I dont see them being top aligned in IE 11, but still, position changes are done by editing the CSS
7) "..so you've replaced the double quotes with $row_reccordsetName['ColumnName']"
yes, that is correct
the other issues I Will have to look at a little later as I have other customers to attend to.