I'm currently taking some HTML code and CSS work I've done and turning it into a wordpress custom theme. I've done this once before but it was a few years back and I'm much more clean with my code now as well as my CSS. When I take my HTML and insert the PHP for my blog to work I've noticed that my webpage goes from working perfectly to a large mess. My header, footer, and content page all slam together at the top. My sidebar I think also covers a majority of the page. I don't see how this is possible when the code works perfectly fine in HTML and CSS format. I've supplied everyone with a link to the HTML version as well as screen shots. This site is not live so I don't have a link to it. If requested I can post code or download links to the code.
HTML & CSS:
When PHP is added: