Hi Tone,
Your set up is correct, but all 3 front screw holes should go through the crank cases.
In fact, after the outer primary chaincase has been fitted you should always turn the engine over very slowly to check that the ends of any of the screws are not in contact with the crank.
I have known folk, after doing complete rebuilds, find that the engine is siezed at this stage and obviously think that it needs to be stripped down again, only to find that one or all of the front screws need to be shortened slightly...or the spacer plate between the crank cases and the inner primary chaincase has not been fitted.
Also, if an engine wet sumps and has been stood for a considerable length of time, the crankcases can fill with oil. Much of this oil can be removed by releasing the bottom front primary chaincase screw and allowing it to be drained off. The remaining oil should obviously be drained via the sump prior to starting the engine.
Beezageezauk.