Wordpress Home page issue

At this point, I can only do changes to my home page at tomwitek.com by doing changes directly to html and uploading it to my server directly. My static page is set in the Reading to Home which was a page I created for displaying the tomwitek.com. The page i used was http://ift.tt/1HVQK3X

Now, I was able to change this page directly using pages panel and it would update the page at Home location. What happens right now is that even though I deleted the http://ift.tt/1HVQK3X at some point the home page was still loading as if the page was there, so now i can only make changes through html.index and only to homepage.

How do I fix this so that it goes back to me being able to do changes through wordpress pages panel instead of doing changes to index.html?

Also, whenever i do changes to index.html (for example I combined 38 css files into 2 (cant get it to one because it breaks my site in IE) these changes are not reflected on my other pages on the site (they still use the original calls for css and js so i get bad Google speed all around)

Which file caused this changes to happen, I am not sure if this was something I did or it happened when there was upgrade to wordpress or upgrade to php?

Help needed.