I don't know why the refrain says "Sing ninety-nine and ninety".
That refrain occurs in the Elizabeth Laprelle/Texas Gladden/Mrs. Rill Martin versions (see the DT and a link in my post of 18 Sept 10) and in a version by Nancy Philley (link in my post of 16 Sept 10), but not in the versions in THE ENGLISH AND SCOTTISH POPULAR BALLADS. It is also missing from the first version I learned, the one that prompted me to start this thread, which was collected in West Virginia by Dr. Patrick Gainer.
In that version, the refrain is "And you so peart* and bonnie". http://www.libraries.wvu.edu/wvconline/patrickgainer.htm
*peart - cheerful and becoming