My experience of this is that there are various methods that are helpful.
1) Make sure you clamp the engine so it cannot move, cover it with something to protect it first.
2) Make sure the flywheel is bolted on tight, and the glow plug is not in the engine, sometimes taking off the back plate helps too.
3) clean and makes sure the flywheel and clutch are clean and smooth, then bolt onto the flywheel.
4) Position the dti as close to the top of the clutch shaft and turnt he engine to see initially how much it is out or not. Some of mine have gone straight on with no probs.
5) Use a piece of chalk to mark the cluthc and flywheel, and using the following options try and get minimal runout on the dti.
Turn the clutch around to see if it is beter boltedon one way or the other, remeasure.
Mark with chalk which side need to be moved close to the centre line, then gently sand that side. Making sure you put the clutch back on the same way round.
Use thin paper to shim out the clutch to alignt he shaft, remeasure.
Last resort if the lower end of the clutch shaft is fine but the top is out, use small movements to bend the shaft to be aligned properly.
Bearing in mind once you have got t aligned, treat it like a live bomb, and knocks to the shaft will put it out again. Get it into the heli and bolted in the correct position asap with as few knocks to the
clutch shaft as possible.
Hope that helps.