What would be the best way to capture someone who is a skilled, experienced fighter with a very high pain tolerance?
A tazer. It doesn’t matter how badass your character thinks they are, when your nervous system is shorted out by an electrical current, you cannot fight.
After that, anything you can use to cripple them quickly, like a crowbar or sledgehammer to the knee will work.
Pointing a gun at their head along with with ten or twenty of your buddies and giving them a choice between becoming the new flavor of chunky salsa sweetmeat or coming quietly is probably your best bet.
If that fails, numbers will end your lone experienced fighter. It doesn’t matter if you’re Jack Bauer or Chuck Norris, you cannot fight a crowd. Combat experience and training can give you the tools to briefly juggle a few people, effectively, but the key word there is, “briefly.”
It doesn’t matter how awesome or badass you think your character is, they can’t take a crowd and win.
Pain tolerance only keeps them going when they’ve suffered an injury that doesn’t actually impair their ability to fight. But, when you’re receiving injuries that are going to make fighting impossible, like breaking an arm, for example, the pain isn’t actually important. You can’t use that arm, no matter how strong your will to fight is.
You can’t make a character superhuman without actually saying, “screw this, I’m giving them superpowers.” The way you take out a lone combatant is basically going to be the same. Overwhelm them.