Hi Carzan,
I have a couple of tricks to help with the alignment of the engine, the pinch style hub should require no dial indicating but the design of the clutch stack does allow you some movement to get a good gear meash and alignment.
I have found the best way to get a good alignment is to have the engine bolted tight to the engine mounts but leave the engine mount bolts that secure then to the frame loose, also leave the clutch stack bearing block bolts loose also. Set the gear meash of the pinion gear to main gear with a slip of paper in between the gear and pinion and then push on the block towards the gear and tighten the bolts, next adjust the engine alignment by lifting it up and down while twisting the start shaft, what you are looking for here is a smooth spot which will indicate the start shaft is in alignment with the engine. Once you have set this tighten up the enigne mount bolts and make sure the start shaft still runs smooth, take out the slip of paper and you should have a perfect gear mech and alignment.
It's not a perfect science but it is something i have used and it seems to work well for me, there is a slight amount of movement in the engine mounts that makes the difference between a smooth spinning start shaft and one that has friction. The friction is caused by the weight of the engine putting pressure on the start shaft.
Hope this helps, let us know how you go with it.
Cheers,
Ross
