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Spazz and I ride the same saddle (Koobi), and mine is also higher than my handlebars, but only about three inches. The one difference is that my seat tilts down very, very, slightly. How do I know? I use a level. I also had to work on the forward/aft position of the seat, about a millimeter at a time, to get it right. It took over a month. But now it's great. So play with positioning for a while.
I bought a new saddle the Serfas Niva for women. 10000000x better already. That and my trico gel shorts(mine not his) solved the soreness problem. I did 8miles this morning and feel great. I didn't want to wait around hoping my seat would get comfy. Seats are cheap enough to try different ones. Besides mine came with a 90day comfort guarantee.
I started out with a stock trek seat - too much padding - your bony areas mash down, pushing the padding in the middle UP into your softer parts. If you want a seat with padding, get one that has the most padding where your bones hit it. Cutouts are another awesome invention!