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If you just want a copy of the site, you can get the httrack extension of firefox (it might be called spider something) from the firefox extensions page (assuming you have the firefox browser, if you don't, get it at mozilla.org), after installing it, go to the homepage of your site and click on 'download site' in the Tools menu of firefox. This will make you a copy of most things in your site - html, images, css - could miss things like links done in javascript or flash. Go through the site and see what's missing. The site's navigation may be somewhat different - but if it's a normal html site, probably not. If httrack doesn't work with the new firefox, just use httrack separately.
You'll also want to get all those files out of root. (you're probably kicking yourself now for not having used a better directory structure). I'd suggest trying the search function you have in windows - you can try criteria like the dates you created the stuff, the extensions you used (like html & jpeg or whatever). If windows lets you select all of these and copy them in one go, you could try that too and see if this gets you any stuff httrack missed.
Welcome to webmasterworld and hope you aren't into too much misery with this task (hopefully someone will find an easier way for you).