The chances are that all your modifications are there but the reason for not seeing them is because your browser is still seeing the old version. After making changes to a theme, you should always carry out the following:
1- be sure that you set "Update module template .html files from themes/your theme/templates directory?" to "YES" in General Settings!
2- Delete all the files (except any index file) in the templates_c folder in the root of your site.
3- Configure your browser to always look for a new version of a website, or
4- Delete all your browsers cached files.
5- Refresh your browser and visit your pages again.
This nearly always remedies the problem. If your changes are still not visible, then it's time to re-check your work.
Re: *sigh*
Fixed it. For some reason, the theme includes weren't dynamic, they were pointing to an old file...now if I can figure out why everything in IE is centered instead of Left align like in Firefox