Does the factory flange have to come off? Might require a new crush sleeve if it does. That means the axles have to come out along with ring and pinion.
NO YOU DO NOT. just torque the flange nut to 40 foot pounds
The pinions depth is set by the shim that is under the pinion bearing all the crush collar and the pinion flange and nut do is allow you to set the correct preload on the two pinnion bearings.
The crush collar sets the preload and the shim under the pinion gear sets the pinnion depth so there is no way to change the pinion depth by changing the pinion flange.
Since these are already set all you have to do is torque to a reasonable number so to put the bearings tight into the races and the crush collar will do its job and stop you from preloading the bearings to much as the crush collar takes huge force to crush any more then it already is..
The only thing that could happen is you could over tighten the new pinion flange nut and then have the pre load be to much wich would preamaturely wear the pinion bearings and possibly cause them howl but would in no way effect the pinion and ring gear as the final depth of them will not change more then a couple millionths of a inch.
However, having done gear setups for 5 years i can tell you that 40 foot pounds is not going to crush that collar any more then it already is it takes 100s of foot pounds of torque to crush those collars down.
We have to use four foot long cheater bars to manualy crush them as we set up pinion preload.
You crush them then check for the amount of torque it takes in inch pounds to rotate the pinion.. once its set to spec its set you can disasemble it and reasemble it torqueing the nut to 40-45 foot pounds without issue unless someone realy torques down on that pinnion flange nut and crushes the collar more..