This saved me what could have (and no doubt would have) ended up being a ton of work. Works great in my theme, which is a modified version of the Twenty-Twelve theme.
Note that if you install it on a network site, it will affect EVERY site. You can, however, set the entire page container as a "no ajaxify" area under the settings page by simply adding the theme's main container ID to the "No ajax container IDs:" list.
Thanks a ton to the developer!
If anyone else doesn't like the scroll down effect when new content loads, you can simply comment out the following lines in "[wordpress]/wp-content/plugins/ajaxify-wordpress-site/js/ajaxify.js".
Found at line 142-145:
//Scroll to the top of ajax container