I haven't had much trouble with the stock seat, but my wife isn't fond of them for much over an hour or two either. When we were going through the process with our motorcycle, we tried a fancy seat overhaul with memory foam that left it soft and extremely comfy. For about an hour -- then it was bailout time. We finally bought a new Mustang seat, which feels very firm when you get on it but still feels fine seven or eight road hours later.
For her, I'm going to try a temporary inch or so of the firmest foam I can get to see if that does it for her. She very rarely travels in the 12, so it may be a few months before I know. Might be worth exploring though. My best advice is to get samples of different densities of foam and try them out for longer trips to see what works for the two of you, before you have permanent changes made.