i have a very similar nagging pain like you discribe...
if someone puts me in a half / full nelson... or does a neck crank submission on me... the next day I have extreme neck pain in my muscles... i usally just use a heating pad and 'ibueprofen' then the pain goes away in a couple days...
Lately it seems that the pain doesn't last as long.... my pain doesn't go all the way down my back like the kind you discribe but it maybe a similar thing....
i have recently learned of a technique that caropracters sometime's use called MAT (muscle activation techniques) i don't know if its gimick or what but people @ my gym have cured a lot of their nagging injuries this way... thought about trying it...
keep us posted on your progress...

good luck!