Hi Kalle,
Your setup for checking the alignment of your crank assumes that the centres in the ends of the shafts are truly in the centre - they may not be! Also, the pressure on the centres may be inducing a false reading.
It is better to support the crank on pairs of ball races, or knife edge rollers, positioned close to the crank webs - then rotate the crank and clock up the small end of the taper and the small end of the timing side shaft. A certain amount of adjustment can be made by squeezing the webs or wedging them apart as necessary. Checking the webs for parallel with a toolbit and feeler gauges will give a good idea where the adjustment needs to be made.
Regards,
Eddie.