1) yes U should include incoming counter on all pages
2) You did not chmod public_html to 777 hence tp_in.php was not added there, just upload empty tp_in.php to your public_html, chmod it 777 and run updater again
3) Source checker checks tarde sites for different malicious parts of code, since its done from our main server it will show results within 24 hrs, it is made that way so your server is not loaded extra then needed