oh well this is just from my experience the last week rebuilding turbos, Mind you they are larger turbos for diesel engines but anyway
shaft/rotor (exhaust wheel + shaft) assembly is cleaned then thrust washers and compressor wheel are installed to the shaft and nut torqued. Shaft is then checked for run-out and the wheel, washers and nut can be rotated/changed whatever to get the minimum run out (the aim for these turbos was 0.02" max), after that the assembly is balanced taking weight off where required (balancing machine is needed for this, very handy) then all compnents marked in there position and removed, cleaned and assembled in the turbo facing the way they were assembled to get the good test results
Basically ensures everything is as straight and balanced as possible
Im sure you could get away with throwing it all back together however, but thats how we did it to get it to near new/new condition. So maybe you get lucky and it works, or maybe it doesnt.... its really one of those your own risk things if u want to do it without the right gear
As i said but this was for a different application to skyline etc so it may be completely different to the procedures used for garett, nissan etc