Tinymce 4 Udate

I recently used this plugin to display some D3 visualizations on posts in my website. But everything I already had got skewed since <\!–mep-nl–> and <code style=display: none; > was being injected wherever there was whitespace. I was able to fix my pages by removing these code injections. But my website formatting has been completely jumbled and I cannot figure out why. Only bottom half of the page elements and footer seems to be acting up. I have removed teh plugin now, but still need to figure out how to restore my original formatting.
Also: I use github and commit my changes daily but unfortunately the WP cache plugin I use prevented us from seeing the breaks before new changes were made and we do not want to lose this work.
Is there something that the plugin changes in my files that I need to remove or do you know how else can I fix this?

This is my site:
Homepage (scroll down after customers) –
http://www.systechusa.com/~systechw/dev/
Contact Page (bottom)-
http://www.systechusa.com/~systechw/dev/company/contact-us/

Any help is appreciated!! Thank you