The are two aspects to pain tolerance. One being physical and one being mental.
It's been proven that when a person has no control over the pain they experience they have a decreased tolerance.
To mentally increase tolerance it's just a matter of *always* pushing yourself past what you thought was your breaking point, even if just a little. Run till you puke, lift ti you puke, hike till you puke, hold your breath till you pass out, etc. The mental aspect of doing this will increase your ability to withstand pain and remain in control. It's not easy and it may take years to develop the correct mindset. During this time you can never stray from the path of misery. Don't wear a coat when it's cold, get wet in the rain, take cold showers, walk when you can drive, wait to pee, run with that blister, don't eat when you're hungry. Everything. Always take the painful way out. Of course that don't mean be stupid and genuinely injur yourself or workout through a REAL injury.
The mental side is very important and you probably won't acheive it alone. People really can't force themselves to be miserable for very long.
The second aspect is the physical side. What I think you're after is called body hardening. Basicly it's nothing more than you and a partner hitting (whith force) different sensitive nerve ending groups, pressure points, and muscles.
These points correspond to where an oppenant will hit you and decapacitate ( a person without body hardening training), surfaces you use to strike with, and surfaces you use to block with.
This training is not fun. It is miserable and must be done on a daily, constant basis in order to work. The spots you harden are very sensitive and you must be struck with a good amount of force 1000's of times.