I would suggest reading the workshop manual for the bike you own before touching it.
You do not apply the front brake,infact i go as far as backing the pads off a tad to avoid any problems from the brakes.
With the front wheel in the air (on a TL1000,i have two) the R/H leg will pretty much seat by itself anyway.
On a TL1000 the wheel is pinned to the left hand fork leg via the axle and threaded collet tube,the pinch bolts retain that collet,the collet is against the R/H wheel bearing which centres the caliper to the brake rotor.
The right hand leg floats on the axle shoulder until retained,the front is bounced so it settles,the pinch bolt are then torqued.
If you apply the front brake they will then dictate the seating of the fork leg,the triple clamp bores dictate that.
Threaded collet held by the L/H forks legs pinch bolts which are not touched when removing the front wheel.
Same set up on the SRAD GSXR's and Hayabusa until 2007.
TL1000 axle,the shoulder pins the wheel to the collet.
I will add this for the TL1000,you better be feeling lucky and know the caliper pistons are working in perfect unison (so they do not move the fork leg ) if you bounce the front with the brake on and weight of the bike on the axle before torqeing the pinch bolts.

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