Well I think 'manliness' to some degree pertains to the alpha male quality in men.
Leaders of others, through physical or social prowess.
Men respect other men with big muscles, because they are strong. Some men dislike or feel less respect for other men who they percieve as being weak or unable to protect themselves.
This 'respect' is probably a very instinctual decision made by humans (dating back to times when strength was needed to survive etc.)
Certain physical features of a man are said to be masculine. A larger nose and squarer jaw. (A larger nose perhaps for better breathing, a squarer jaw denoting a better fighter etc.)
The higher pain tolerance you mentioned would also fit into the area of a skill needed for basic survival.
So basically, 'manliness' is a quality attributed to those better able to survive a certain or set of situations.
At least that's all that popped into my head in the 2 mins it took to write this reply 
