There are alignment tools that will check for and correct fork and frame misalignment. The Park FFG-2 is one such tool and any good bike shop should have one but it's too expensive for a one time home user to bother with. Find a bike shop with the Park or similar tool and let them do the job for you.
BTW, caliper brake front wheels are not "dished" (i.e. have the rim offset between the hub flanges) like most rear wheels but should be symetrical and the rim centered between the flanges. If you had to build the rim off center, the fork is indeed not aligned properly.