I did the same thing, and I am still working through it too. I will keep posting as I go. I just found out the mega menu is not responsive. What I did was keep the mega menu for my desktop and put this code below in responsive.css and responsive_mobile.css. Not sure if you made a custom template or not. If you did copy those two files in your custom template css folder with the changes.

@media (min-width:0px) and (max-width:480px){ #mega-wrapper { display:none;visibility:hidden; }

Now the problem I am working on is this works until they get to the product info page, then the menu is loosing the css. That may be do to other changes I made. I would be interested if you do not have that problem if you try my fix. That may head me in the right directions too.

Good Luck hope this helps. And I will keep updating as I figure it out.