Tip for startups - buy a filing cabinet and a bunch of folders. Come up with some system - any system - it doesn't really matter. The worst one is better than none at all. Put everything in there and don't worry about cleaning it out. I'm talking about all your insurance crap, leases, property records, blah blah...things that are not "core business"
If you want to go paperless, get a Fujitsu ScanSnap for $400 and scan everything to Evernote - or a Directory Tree - or some other DMS. You'll make life EASY EASY when compared to the alternative of having someone like me in your office for 3 weeks keeping you from running your company while I piece back together everything you've shredded.
EDIT: oh yeah - don't try and "hide" shit. M&A guys are experts at sniffing out things you're not telling us, intentional or simply forgotten. I've got forensic accountants who are incredible at their job sifting through everything under the sun finding this stuff. Most of the time, you just forgot, and thats fine. Everyone does. If you're trying to hide a skeleton, we're gonna find it. Talk to the M&A guy who's on your side (the sellers side) and be honest. We've got a better chance of presenting the information honestly that won't alter the deal.