OK, dealing with removal and re-installation of the forks starts on page 4-73 of the service manual. The process goes on for a number of pages as it concerns total servicing of the forks.
The manual calls for tightening the two lower bracket pinch bolts first and the doing the upper bracket pinch bolt. If you have received your forks back with the cap bolt already fastened, I suspect this really doesn't matter because it is the reverse of the removal procedure and the removal procedure has you leave the upper bracket pinch bolt tight so you can remove the cap bolt without putting the fork in a vice.
For what it's worth, I slide the fork leg in and hand tighten the upper bracket bolt to hold the fork in the position I want it in. Then I hand tighten the two lower pinch bolts. Then do the same to the other fork leg and check that both forks have the same reveal at the top. I like to place them so that the edge of the cap bolt is just above the bracket. Next, finagle your torque wrench onto the lower bolts and snug them to the proper spec (23Nm). With the forks held firmly, now would be the time to torque the cap bolts to 25Nm. Move up to the top bolts and snug them up to 25Nm. If you had removed the steering stem nut, torque it to 115Nm.
If you are also interested in the axle pinch bolts, read on. Looking from the front of the bike, the axle pinch bolts are numbered, right to left 1 through 4. The tightening sequence is 2-1-2, then 4-3-4. Tighten each bolt to 21Nm without temporary tightening. Normally, I go back and forth a couple of extra times so that the torque wrench clicks without any bolt movement.
Hope this was a help.
Dan
