It may have been John with the psychosomatic limp, but it is Sherlock who ages into pain. All of that running through London's streets was bound to take a toll, and there's only so much wear and tear that retirement can ease.
At first it was tiredness - bone-deep exhaustion, in fact - that brought on the aching in his knees. He'd doze off on the couch or in his chair or in bed while John carefully massaged his afflicted joints, through the fabric or otherwise. Then the cold began to trigger the humming pain. This was found to also be soothed by similar tender ministrations of John's.
Mostly recently, however, Sherlock's pains have been associated with the storms. Right elbow - minor, no need to worry. Right knee shooting into shin - batten down the hatches. Left knee and shin - ensure the bees are secured and retreat to bed with John to sleep through the meteorological event. Though he's never put much stock in such unscientific methods of divining the weather, Sherlock has begrudgingly admitted that there appears to be evidence of his physical self responding to atmospheric shifts.
(John, for his own part, is quietly amused for the suffering of his dear lover. Of course it was always going to be Sherlock with a barometer of a body.)