I don't have IE8 here atm, so haven't tested it but I noticed that you're using Modernizr and Respond.js. Have you tried downloading the production version of Modernizr (there's a checkbox there so it will include respond.js automatically). That might solve some incompatibility issues which may or may not cause the not firing of the media queries.
Have you checked the loading order css vs js ? If the respond.js gets fired before the css gets loaded you might want to defer script loading or place it at the bottom of the master page.
Secondly, I'm not sure I fully understand the problem with two css files, if you move them to a rootfolder, you don't have to leave them in App_Data no?
But if you'd like to stick to SF and store everything in the App_Data folder, you can always reference it directly. Next to the App_Master and App_Theme folder inside of 'Aardvark' I often create a JS folder that contains specific theming stuff and reference it by src="/Sitefinity/WebsiteTemplates/MyTemplate/JS/script.top.min.js"
VisualStudio will give you an error that the file won't exist, but besides that, works like a charm.