Thats alot of sitting trainer time. Do you get out of the saddle while riding? I have recently been riding the trainer alot and I try to change positions on the bike. In the hoods, in the drops, on the bars and even without hands I lean back. Also getting out of the saddle every few minutes helps. Try a couple of pairs of shorts, maybe a little extra butt bone cushion until things toughen up.
Just my two cents, I use a specialized ruby saddle, flat but with a great cutout and no edges. Those SMP saddles look like they could hurt with the raised inside edges.