My neck muscles went at 1050Km and had to deal with that till the end. Also have numb hands and toes/balls of feet.
Something I wonder is whether riders do enough neck strength work; race drivers in training build up their neck muscles so that they can deal with the weight of their head+helmet in the conditions encountered in a race car.
The most basic version of this I've seen described was David Coulthard lying on the floor in front of the telly with his helmet on, raising his head while lying on his left side for a while and then switching over.
While cycling doesn't require you to be able to keep your head under control when it's weighing 5 to 8 times it's mass on a number of axes, being able to hold it up at angles that allow you to see does seem to me to be part of training required.
Note: I've never suffered from neck problems while cycling and the closest I do to training my neck is hold the head in front of a computer screen all day.
discomforts:
My dodgy right ankle is a bit worse than normal, I tweaked it while wandering around the Bergerie in SPD-SL shoes on SAturday.
Hands, my hands were fine until I swapped into my "night" gloves; I'll be disposing of them and switching to a selection of Altura classic styled gloves now.
Feet, despite the late change to new shoes my feet hardly suffered, there was some size change with swelling though, and my wider (but shorter) right foot suffered from being squeezed in a shoe that became too narrow, and my longer but narrower foot suffered from being squeezed in a shoe that's too short.
Which is some amount of swelling.
other than that general aches and pains from sleeping on floors, tables and under trees that dissappeared after a rest.