i would suggest that the dull ache probably is musclar but as this is the internet hard to tell, but go to an osteopath (peopel will recommend physios/osteopath and chiropracters based on their experiences, having used all three i would only go to an osteopath) they if any good will tell you about alingment and core strength and probably ease or remove the pain but importantley tell you hands oin what the issue could be.
Core srength work is vital anyway as is stretching, needs to be regular and consistant to have any impact and longevity. Also look at strength in legs, all to be with alingment. General posture as well. Walk tall and so ………
Shorter stem, will affect plus spacers as will saddle type height. Bars make a difference as well. Try a cheap suspension post USE i prefer rather than thudbuster but again personal preference.
On the bike silly as it sounds stand more use the knees and arms to absord impact, relax……and all that flow stuff, tensing up really knackers one.
oh and sell the hardtail for a nice full suss… 😉