That "shaft coming off the fork" is called the steerer tube. They're typically cut so that they'll extend up out of the frame's head tube just far enough to accept the headset and stem, plus maybe a few spacers. It sounds like the fork you received was cut to fit a smaller frame than the one you're trying to install it into. Unfortunately for you in this case, steerer tubes generally aren't swappable. They're an integral part of the fork and not meant to be removed and refitted.