The newer engines use a two piece ignition side roller bearing (like KTM engines), vs. the ball bearings on the older bikes like roost's bike. These bearings run, by design, at a greater clearance and therefore may (will?) cause slightly more vibration.
As far as the crank positioning, it should be done by drifting the crank in the bearings, not the bearings in the cases. Some older bikes like my '00 had a very loose fit and the crank would float in the bearings, eventually wearing the journals even more and requiring replacement. This was a problem on some cranks in '99-'00.
If you want to split the cases and rebuild the lower end, measure the total clearance between the crank wheels and the cases(the sum of both sides). When you assemble the motor, divide this by two and place a feeler gauge of this dimmension in the case for the crank to seat against when you fit it in on the primary side. This will give you an approximate center with no tapping on crank to adjust later. This is how I do it, not neccessarily a documented procedure.
FWIW, I always use heat/cold instead of force to assemble an engine. Warm the cases in an oven and freeze bearings with dry ice, it will go together with much less trauma. Same with the crank, warm the primary side case with the new bearing, freeze the crank, and it will fall right in.
Hope this helps.