I would strongly suggest picking up a few of these sorting trays. It will cut down on your set sorting time significantly.
Card Sorting Tray / Display for Sports and Non Sports Cards / Magic / Yu Gi Oh | eBay
Generally when I have a very large break like this, I will sort everything out by 100's, then 10's, and finally single cards. Start building the sets from the bottom card up, taking notes on each pile if there is an incomplete set or 2. For me this is a significantly quicker process.