I think your body is telling you, you need a break. You didn't say how often during the week you ride. So just on a guess, you may be pushing yourself too much.
Try not riding for a couple of days, let your body recharge then try again but do it easy and work your way back up to 6-10 miles.
As for arms/shoulders hurting and the seat bothering you makes me wonder if you were professionally fit on your bike. In the end back off a bit and see what happens.