Look for any soft spots in the floor, walls and roof. Any discoloration and don't forget to check the backs of cabinets. Check inside the underbelly as well for insulation and/or wood damage. They could have replaced plywood and left a mess underneath. I'd also insist on a pressure test on their dime to prove the leaks have been repaired.
On top of that I'd negotiate HARD. A few thousand below market wouldn't cut it for me. Remember the next guy will do the same to you if you go to sell it down the road.
