I did exactly that with several boxes. Only a couple had wire nuts pointing down, so I fixed them. Also used silicone sealant to seal around the gray conduit where it entered the top of any boxes.
Good idea about how to find the culprit -- start at the halfway point. Then depending on the result, go to halfway along one of the two legs, and keep doing that until you find it. In computer jargon it's called the binary search method, and is one of the fastest ways to find something. There is a game that works the same way -- have someone think of a number between 1 and 100, then tell you if your guess is low or high. Using the binary technique you can always guess the number in about 7 tries.