So for some reason or another it was the padding. I made a stylesheet specifically for IE7 that has:
*{padding:0 !important}
Then I manually went through the website and re-styled each element with my own padding and none of Bootstraps (in that IE7.css file). It works now and there's no crazy flashing or anything and I'm feeling good.
If anyone else comes across a similar problem I put this in my header:
<!--[if lt IE 8]>
<link href="<?php echo get_template_directory_uri(); ?>/css/bootstrap-ie7.css" rel="stylesheet">
<link href="<?php echo get_template_directory_uri(); ?>/css/ie7.css" rel="stylesheet">
<![endif]-->
It's a lot of tedious work and I hate IE except 11 isn't that bad. Unfortunately my client's building is still using IE7 so I had to unwillingly support it.