1. Loosen the front axle clamps, and the axle nut.
2. Loosen the lower triple clamp bolts.
3. Grab a handfull of front brake. Pump the forks up and down several times, pushing them as far down into the travel as you can. You'll feel the action get smoother as the tubes re-align themselves.
4. Tighten the triple clamp bolts first. Use a torque wrench. Over-tightening these bolts by even a small amount distorts the tubes slightly, which will cause the bushings to pinch as the forks compress, causing a harsh mid-stroke spike in the fork action. Over-tightening these bolts by a lot will break the clamps.
5. Tighten the axle by holding the nut and spinning the axle with a hex socket on a torque wrench. This will ensure that the axle is perfectly aligned in the forks. Always use a torque wrench. Over-tightening the axle will shorten the life of the wheel
6. Tighten the axle clamps.
This method will ensure perfect fork tube alignment, which will in turn ensure correct front wheel alignment. If the wheel and fork tubes are still mis-aligned after this, then either a fork tube or a triple clamp is bent.