Never heard so much bad front end/suspension advice in my life!!! If you want to align your front end the RIGHT way:
1. Set fork height in top triple clamp properly (I use a dial caliper to do the measurement). Tighten the top clamp only.
2. Mount the front wheel. I tighten the pinch bolts (bottom of the fork to the axle) opposite the axle nut first, then tighten the axle itself.
3. Tighten the pinch bolts on the axle nut side, then LOOSEN the ones opposite the axle nut.
4. Tap (gently) a slim standard screwdriver or other appropriate "wedge" in the slot in the bottom of the fork "pinch clamp" (same side you just loosened) to allow the axle to move freely back and forth.
5. Verify that the fork will also move freely in the LOWER triple clamp by facing the front number plate and moving the handlebars back and forth.
6. Take the bike off the stand and forcefully compress the front end while grabbing a handful of front brake. This aligns the forks in the triple clamps and the front axle (after removing the screwdriver of course). I usually do this 5-6 times to insure that everything is free-floating with no restrictions.
7. CAREFULLY put the bike back on the stand, tighten the lower triple clamp and axle pinch bolts to spec (usually ~14 ft lbs).
8. Go ride. :ride: