Kalle,
The factory practice with the S6 crankshaft (and probably others from the EW to the Aero) was to get it very closely aligned, pin the joint, and then do the final grinding of the main journals. For it not to line up, the throws have to be sprung or it is a crankshaft built up from components of more than one crankshaft.
First, study if springing the crank as Bert suggested will bring it closer to true. If it needs a radial twist and the pins are preventing you from doing that, the accepted practice is to remove the pins, do the alignment, and then re-bore the pin holes for a slightly larger dowel (like 5mm).
Do not be tempted to leave the pins out, you cannot tighten it up enough to stop it from slipping.
-Doug