Where are you starting from? Will you be camping? Can provide some suggestions for good spots to visit as I've spent a good deal of time in the Western Isles, including several times south to north. Have even a written a book on the subject - http://www.amazon.co.uk/Photographers-W ... 0859767043
If you have the time, you can make a day trip south from Castlebay to Mingulay, an island that was evacuated in the early 20th century. Also, and again if you have the time (and in this case the £s too), you might consider taking a day trip to St Kilda from Leverurgh, Harris, or from near Uig on west coast of Lewis with Seatrek.
If camping, the machair at Vatersay would be a nice spot for your first night. If needing accommodation, you probably know about the Gatliff Trust hostels already, but might be worth mentioning you can camp at each spot too (Howmore, South Uist; Berneray; and Rhenigidale, Harris).
I've mentioned the west coast of Lewis already. If in tent, wild camping on the hills above Mangursta beach is great. Also, there's a camping spot with limited facilities next to Uig sands.