The most important thing about cleaning a gun comes from breaking it in. If you look at a magnified bore on a factory gun it will look like thousands of jagged edges. These edges all catch fouling, copper, lead, etc. Custom barrels have typically been lapped and are free of these. The best way is to start fresh if you have a gun that has been fired and possibly abused.
Clean gun with sweets or Hoppes ora good copper solvent
Then clean it with JB Bore paste
shoot the gun
after each round run a brush through the barrel several times
after ten rounds clean again with sweets or other solvent
fire another 10 rounds
fire another ten rounds and run brush through after each round
clean thoroughly with sweets or hoppes
use the JB bore paste again
fire a fouling shot
then fire a 3 shot group for accuracy
some good info here:
http://www.6mmbr.com/borebrushing.html