When I got my Fatboy in 1999, I had a hard time with my seat as well.
I had a guy swap out the foam from HD and add car seat foam (or something like car seat foam) and then they re-installed the same leather that came on the bike. It was a cheap alternative and the seat has held up well for over 4 years now. I have about 18,000 miles on that seat now and I do some long rides. I can ride for 8-10 hours and my rear is fine. The guy charged me $150.00 to swap out the foam, and it still looks like the orignal stock seat. Maybe this can be an alternative for you.