Template file printing on every page
I'm pretty certain you want to be saying 'template' in your  hook_theme():

template: If specified, this theme implementation is a template, and this is the template file without an extension. Do not put .tpl.php on this file; that extension will be added automatically by the default rendering engine (which is PHPTemplate). If 'path', above, is specified, the template should also be in this path.

instead of 'file', as...

file: The file the implementation resides in. This file will be included prior to the theme being rendered, to make sure that the function or preprocess function (as needed) is actually loaded; this makes it possible to split theme functions out into separate files quite easily.

...which would suggest the reason why all of this html is being spit out on top of each page because it is being included every time instead of being buffered with Drupal's theme engine as a template and then output later on.