Wow! That's a serious distance. Especially on a MTB! Well done!

Having pain during or after cycling isn't funny. I sometimes have pain in my shoulders after long rides, but that's mainly because I forget to relax my arms. I keep them overstretched too much during rides. The elbows need to be in a slight angle to absorb shocks. I tend to forget that sometimes.
Since it's your back and neck you might not be in the right angle. You could try adjusting your bicycle a bit.