Re: removing the "tiki-index.php?" from URL
You can implement sefurls (rewrite rules + smarty outputfilter)
The rewrite rules are enough for your email problem
You have already in the file _htaccess in your tikwiki root directory that you need to copy the lines into .htaccess (hoping your hosting allows that..)
To not create links with tiki-index.php, you can use a smarty outputfilter as described in various page as SEFURLs
like this instead of www.domain.com/tiki-index.php?page=WhatEver will be www.domain.com/WhatEver.
With the output filter no need to edit all the tikiwiki page.
;){kind=link}
;){kind=link}