A recent One Big Happy:
Higher vs.lower, in several senses. The two families of pain in the idioms are high vs.low on the body and high vs. low in tone. (They’ve been around for about a hundred years, but apparently didn’t catch fire until the 1930s.)
From GDoS, high end first:
pain in the neck (also head, side) 1 a feeling of irritation 2 an annoying person, a bore, a euph. for pain in the arse [first clear cite in 1926 (Carl Van Vechten)] 3 an annoying situation, anything considered unpleasant, typically a task one does not wish to perform [first cite in 1940 (Cab Calloway)]
give someone a pain in the neck etc. [earlier give someone a pain, an ache (with no location specified); then a first clear cite in 1911]
Then the low end:
pain in the arse (ass, backside, butt, can, fanny, etc.) 1 a feeling of irritation; usu as give someone a pain in the arse [first cite in 1935] 2 an annoying person [first cite in 1934 (Clifford Odets)] 3 an annoying object, situation or circumstance [first cite in 1951 (Mickey Spillane)
Google Ngram shows pain in the neck at modest levels going way back, but presumably in reference to literal pains. It then shoots up in the 1920s. On the other hand, pain in the ass doesn’t really shoot up until the 1960s and 70s; eventually it substantially overtakes pain in the neck — no doubt a reflection of greater directness (or, if you will, crudeness) in speech over these years. Now, it seems, even little kids like Ruthie know the gluteal variant, and also know that it’s not something you’re supposed to say in polite company.