My general though on this whether using a house wide theme or random themed rooms, you need to know what your most intense scares will be (The Highs) and what the less intense scares will be (The Lows).
You dont want all the best scares in the first part of the haunt and I would say you dont want them all in the last part either. In a perfect world I would try and find a balance to the scare intensity just to keep them guessin. Plus if you have a "LOW" followed by a "HIGH", it will make the intense scare seem that much better. The last few rooms of the haunt I would try and built the entensity of the scare so that the last room will be one that your guests remember as a great scare. As ultimately your guest will judge your haunt by the last few rooms.