We marked the shaft and wheel before disassembly. It went back on exactly as it came out so should be ok. In an ideal world with a few more poinds to spend you'd get it dynamically balanced but not on a kitchen table rebuild.
@Cov: There are loads of videos on the net about it. It's pretty simple once you get in there. Take the housings of both sides. Undo the bit on the compressor end whilst holding the ehaust end (reverse thread on these), tap shaft to pop it off the oil seals. You then have a circlip holding on a retaining plate. Once that's off you will see the thrust bearing held down by 3 screws, take these out and remove the thrust bearing. Under that is the first journal bearing, then circlip, then another circlip and another journal bearing. If you set the shaft up on the table and thread everything you take out in order into that its much easier to reassemble. You've also got 2 oil seals, one on the shaft (exhaust side) and one on the bit that slots into the thrust bearing. Assembly is reverse of removal.
I like to put one new bit on and then chuck the old one from the shaft into a tray. You know where you are then.
These are really simple bits of kit. Once you've done one you'll be able to do another one twice as quick.