It could be fit or saddle...but I also think the upright position is inherently less comfortable over distance; at least it is for me. I think the best answer is to switch it out to drop bars...there are a bunch of bar and stem options designed to make a MTB a drop bar bike while still retaining the extra leverage of flat bars, and this gives the more familiar position and multiple hand positions. When I shift hand positions I also typically shift on the saddle, which I think relieves pressure. You'll have to get new brake levers and shifters, but I think the end result (comfort) will be worth it.

Full disclosure - I'm biased because I'm building my first drop bar MTB right now and am very enthusiastic about it.