QCD
Check the following sites, these organizations publish the standards you are looking for.
Be aware that tolerances is construction/design characteristics of the machine and this can vary with the OEM. Check with OEM for this and other pertinent data on this type of job.
I am a bit confused, the deviation in height is along the center line (axially) or from the center line (radially)?
I will assume the deviations are from the center line as stated by you in the last sentence.
Those 0.1” deviations were in the original machine or are new due to the refurbishing? Are those deviations are with the poles installed in place? If so, check if the pole is seating properly against the rotor spider, this can be a problem.
Most important is the mechanical and electrical balance of the rotor, you are right saying that the poles ideally must be in the same place for keeping the original balance.
You might put steel shimming under the rotor poles to compensate the height but you can upset the mechanical balance of the rotor, again check with the OEM on this.
Averages might be misleading, for example, if most of the deviations are in the same region of the rotor, the rotor gap will not be uniform along the circumference; you can plot the deviations in a graph or table to check this
The rotor must be in the mechanical centerline of the stator bore this will insure a uniform gap in the generator and your bearings will last longer, generally this is done at the factory during construction and does not change but it is wise to verify it.
Be sure to perform pole voltage drop test to insure the magnetic balance of the rotor, there are also other tests done with this type of job depending on the client. I hope this helps.