It sounds like you're having some fit issues with your bike. I'll let others go into more details about that, but you can just play with the various adjustments, different saddles, stems, and so forth, and figure out what fits for you. If I was commuting 25 miles each way on a mountain bike I'd also want some bar ends so I had another place to put my hands.

You also might want to consider a rack and panniers instead of a backpack.

And for riding 50 miles in a day, I'd also recommend something with a chamois. They make mtb shorts that are relatively inconspicuous (Fox, I think), but for that kind of distance I'd honestly just go for full on cycling shorts, 3/4 or full length tights. I've never found anything that was loose and had a chamois to be comfortable; it feels like you're wearing a diaper.